# HG changeset patch # User stef # Date 1410426671 14400 # Node ID 9285f791716dadd55e22e2781cec5fb27bc22598 # Parent 1b81dd6b68b55dc1c76421caabbd2bdcfb31b613 Uploaded diff -r 1b81dd6b68b5 -r 9285f791716d README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,30 @@ +Falco Amplicon Analysis Pipeline & Galaxy wrapper +======================================== + +Text + + +History +======= + +============== ======================================================================== +Date Changes +-------------- ------------------------------------------------------------------------ +September 2014 * first release in Tool Shed +July 2014 * first release in Test Tool Shed +============== ======================================================================== + +Tool Versioning +=============== + +Tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta. + + +Bug Reports & other questions +============================= + +Issues can be reported via the contact form at diff -r 1b81dd6b68b5 -r 9285f791716d falco.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco.sh Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,138 @@ +#!/bin/bash +TOOLDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" + +echo "Start falco sh" + +## ---------- +## Variables setup +## ---------- +#bam_file=$1 +#bam_name=$2 +#html_out=$3 +#vcf_out=$4 +#out_path=$5 +source $1 + +bam_base=`echo $bam_name | sed 's#.bam$##' - ` + +## ---------- +## Create extra init script +## ---------- +#if [ $design_file != 'None' && $design_file != '' ]; then BED_PATH=$design_file; fi +#if [ $manifest_file != 'None' && $manifest_file != '' ]; then MAN_PATH=$manifest_file; fi +if [ $design_file != 'None' ] # Galaxy default is "None" +then + BED_PATH=$design_file +else + BED_PATH="$TOOLDIR/tool-data/GALAXY_TSACP.bed" +fi + +if [ $manifest_file != 'None' ] # Galaxy default is "None" +then + MAN_PATH=$manifest_file +else + MAN_PATH="$TOOLDIR/tool-data/GALAXY_TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt" +fi + +echo "BED:"$design_file +echo "MAN:"$manifest_file +echo "BED chosen:"$BED_PATH +echo "MAN chosen:"$MAN_PATH + +init_file="galaxy_init.sh" +echo '#!/bin/bash' > $init_file + +## executables +#echo "snpEff=/ccagc/lib/snpEff/snpEff_v3_4" >> $init_file +echo "snpEff=$SNPEFF_JAR_PATH/" >> $init_file +#echo "snpSift=/ccagc/lib/SnpSift" >> $init_file +echo "snpSift=$SNPEFF_JAR_PATH/" >> $init_file +#echo "varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar" >> $init_file +echo "varscan=$JAVA_JAR_PATH/VarScan.v2.3.5.jar" >> $init_file + +## files +echo "targetBed=$BED_PATH" >> $init_file +echo "manifest=$MAN_PATH" >> $init_file + +## ---------- +## Status / debug +## ---------- +echo "BAM: "$bam_file +echo "OUT: "$bam_name +echo "BAMBASE: "$bam_base +echo "OUTPATH: "$out_path +echo "HTMLOUT: "$html_out +echo "VCFOUT : "$vcf_out +echo "INIT : "$init_file + +## ---------- +## create output files dir +## ---------- +mkdir $out_path +mkdir $out_path/$bam_base + +## ---------- +## running analysis +## ---------- +echo "Starting VcAn" +$TOOLDIR/falco_new/amplicon-VcAn-TSACP.sh $bam_file $bam_base +#$TOOLDIR/falco/amplicon-AlVcAn-TSACP.sh ## this contains more + +echo "Starting amplicon-Report" +$TOOLDIR/falco_new/amplicon-Report.sh $bam_base + +echo "Starting QC" +$TOOLDIR/falco_new/amplicon-QC.sh $bam_file + +#echo "Starting plots.R" +#$TOOLDIR/falco/misc/plots.R $bam_base.qc.ann.txt $bam_base.qc.targets.txt $bam_base.pdf + +echo "Starting mkHtmlReport" +$TOOLDIR/falco_new/misc/mkHtmlReport.pl ./ ./ + + + +## ---------- +## create index html for main galaxy output +## ---------- +echo "" >> $html_out +echo "" >> $html_out +echo "" >> $html_out +echo "" >> $html_out +echo "" >> $html_out +echo "" >> $html_out +echo "

FALCO

" >> $html_out +echo " HTML" >> $html_out +echo " " >> $html_out +#for file in *.vcf *.txt *.tsv +for file in * +do + lineCount=`wc -l $file | cut -f 1 -d " "` + echo " " >> $html_out + #echo " " >> $html_out +done +echo "

$file has $lineCount lines

HEAD: " `head $file` "

" >> $html_out +echo "" >> $html_out +echo "" >> $html_out + +## ---------- +## creating galaxy history outputs +## ---------- +#cp 'index.html' $html_out # this is the overview of samples html +cp $bam_base'.html' $out_path/'out.html' # this is the sample html +cp $bam_base'.vcf' $vcf_out + +## ---------- +## copy files to keep to output path +## ---------- +cp -r ./$bam_base/*png $out_path/$bam_base/ +cp -r ./* $out_path +#cp *.vcf $out_path; cp *.tsv $out_path; cp *.txt $out_path; cp *.html $out_path + +## ---------- +echo "END falco sh" +exit 0 \ No newline at end of file diff -r 1b81dd6b68b5 -r 9285f791716d falco.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco.xml Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,120 @@ + + + + + samtools + R + snpeff + VarScan + + TOOL_DIR + + + FALCO: Amplicon Analysis Pipeline + + + + + + + + falco.sh $falco_cfg; + + + + + + + + + + + + + + + \S+ + + + + + + + + + + + + + + + + + + + design_file=$design_file + manifest_file=$manifest_file + bam_file=$bam + bam_name=$bam.name + html_out=$html_output + vcf_out=$vcf_output + out_path=${html_output.files_path} + + + + + + + + + + + + + + + + + + +.. class:: infomark + +**Introduction** + +This tool is a wrapper for the Amplicon Analysis Pipeline (AAP) FALCO_ + +.. _FALCO: https://bitbucket.org/daoud/falco + +Calls and annotates genomic variants for each amplicon in a design. + +----- + +**Citation** + +For the underlying tool please cite: Daoud Sie et al. Title TBA (submitted). + + + + diff -r 1b81dd6b68b5 -r 9285f791716d falco/README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/README Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,31 @@ +# +# Author Daoud Sie +# e-mail d.sie@vumc.nl +# +###### + +Let's put some useful stuff here... + +The Amplicon Analysis Pipeline (AAP) takes fastq files as a starting point. However, each +stage of the pipeline can be run separately. + +amplicon-Al-TSACP.sh R1.fq R2.fq output + +This will run the following: + +- flash read merging +- adapter clipping +- quality trimmer +- alignemt using BWA + +- amplicon-VcAn-TSACP.sh +-- variant calling and annotation: +-- samtools variant caller +-- custom variant caller +-- snpEff effect prediction +-- dbSNP annotations + +- amplicon-Report.sh +-- filtering of variants +-- report generation + diff -r 1b81dd6b68b5 -r 9285f791716d falco/amplicon-Al-TSACP.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/amplicon-Al-TSACP.sh Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,105 @@ +#!/bin/bash + +DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" + +source $DIR/init.sh + +TMP=./tmp +if [ ! -e $TMP ] +then + mkdir $TMP +fi + +fq1=$1 +fq2=$2 +output=$3 + +bfq1=`basename $fq1` +bfq2=`basename $fq2` + +if [ ! -e $TMP/$bfq1.trim ] +then +echo `date` " [$$] - $adapt_clipper -a $illmP5 $fq1 > $TMP/$bfq1.trim" +$adapt_clipper -a $illmP5 $fq1 > $TMP/$bfq1.trim +echo `date` " [$$] - Done!" +fi + +if [ ! -e $TMP/$bfq1.qtrim ] +then +echo `date` " [$$] - $qTrim -t30 -i $TMP/$bfq1.trim -o $TMP/$bfq1.qtrim -Q34" +$qTrim -t30 -i $TMP/$bfq1.trim -o $TMP/$bfq1.qtrim -Q34 +echo `date` " [$$] - Done!" +fi + +if [ ! -e $TMP/$bfq2.trim ] +then +echo `date` " [$$] - $adapt_clipper -a $illmP7 $fq2 > $TMP/$bfq2.trim" +$adapt_clipper -a $illmP7 $fq2 > $TMP/$bfq2.trim +echo `date` " [$$] - Done!" +fi + +if [ ! -e $TMP/$bfq2.qtrim ] +then +echo `date` " [$$] - $qTrim -t10 -i $TMP/$bfq2.trim -o $TMP/$bfq2.qtrim -Q34" +$qTrim -t30 -i $TMP/$bfq2.trim -o $TMP/$bfq2.qtrim -Q34 +echo `date` " [$$] - Done!" +fi + +if [ ! -e $TMP/$bfq1.qtrim.paired ] +then +echo `date` " [$$] - perl $pairUp $TMP/$bfq1.qtrim $TMP/$bfq2.qtrim" +perl $pairUp $TMP/$bfq1.qtrim $TMP/$bfq2.qtrim +echo `date` " [$$] - Done!" +fi + +# FLASH Fastq joiner +if [ ! -e $TMP/$output.flashed.fq ] +then + +$flash -r150 -f180 -c $TMP/$bfq1.qtrim.paired $TMP/$bfq2.qtrim.paired > $TMP/$output.flashed.fq + +fi + +#if [ ! -e $TMP/$output ] +#then +#echo `date` " [$$] - $stampy -g $index -h $hash --readgroup=ID:$output,SM:$output --gatkcigarworkaround --bwaoptions=\"$bwaref\" --bwa="$bwa" --bwamark -o $TMP/$output -M $TMP/$bfq1.qtrim.paired $TMP/$bfq2.qtrim.paired" +#$stampy -g $index -h $hash --readgroup=ID:$output,SM:$output --gatkcigarworkaround --bwaoptions="$bwaref" --bwa="$bwa" --bwamark -o $TMP/$output -M $TMP/$bfq1.qtrim.paired $TMP/$bfq2.qtrim.paired +#echo `date` " [$$] - Done!" +#fi + +# Added -e 40 for maximum indel size of 40,... +#if [ ! -e $TMP/$output ] +#then +#echo `date` " [$$] - $stampy -g $index -h $hash --readgroup=ID:$output,SM:$output --gatkcigarworkaround --bwaoptions=\"-e 40 $bwaref\" --bwa="$bwa" --bwamark -o $TMP/$output -M $TMP/$output.flashed.fq" +#$stampy -g $index -h $hash --readgroup=ID:$output,SM:$output --gatkcigarworkaround --bwaoptions="-e 40 $bwaref" --bwa="$bwa" --bwamark -o $TMP/$output -M $TMP/$output.flashed.fq +#echo `date` " [$$] - Done!" +#fi + +if [ ! -e $output.bam ] +then +echo `date` " [$$] - $bwa aln -e 40 $bwaref $TMP/$output.flashed.fq > $TMP/$output.sai" +$bwa aln -e 40 $bwaref $TMP/$output.flashed.fq > $TMP/$output.sai +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $bwa samse -r \"@RG\\tID:$output\\tSM:$output\" $bwaref $TMP/$output.sai $TMP/$output.flashed.fq > $TMP/$output.sam" +$bwa samse -r "@RG\tID:$output\tSM:$output" $bwaref $TMP/$output.sai $TMP/$output.flashed.fq > $TMP/$output.sam +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $samtools view -uS $TMP/$output.sam | $samtools sort - $output" +$samtools view -uS $TMP/$output.sam | $samtools sort - $output +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $samtools index $output.bam" +$samtools index $output.bam +echo `date` " [$$] - Done!" +fi + +echo `date` "[$$] - $VcAn $output.bam $output" +$VcAn $output.bam $output +echo `date` "[$$] - Done!" + +echo `date` "[$$] - $report $output" +$report $output +echo `date` "[$$] - Done!" + +exit diff -r 1b81dd6b68b5 -r 9285f791716d falco/amplicon-AlVcAn-HaloPlex.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/amplicon-AlVcAn-HaloPlex.sh Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,127 @@ +#!/bin/bash + +index=/scratch/data/ref/hg19/stampy/hg19 +hash=/scratch/data/ref/hg19/stampy/hg19 +bwaref=/scratch/data/ref/hg19/bwa-5/hg19.fa + +adapt_clipper=/opt/cutadapt/cutadapt-1.1/bin/cutadapt +illmP5="AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" +illmP7="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT" +qTrim=/opt/bin/fastq_quality_trimmer +pairUp=/storage/shark1/data/Git/ampliconPipeLine/pairUp.pl +stampy=/opt/stampy/stampy-1.0.18/stampy.py +samtools=/opt/samtools/samtools-0.1.18/samtools +pileup2cov=/storage/shark1/data/Git/ampliconPipeLine/pileup2cov.pl +attachManifest=/storage/shark1/data/Git/ampliconPipeLine/attachGff.pl +manifest=/scratch/data/ref/manifests/HaloPlex/Analyzable-region-01355-1335878719.gff +snpEff=/opt/snpEff/snpEff_3_0a + +plots=/storage/shark1/data/Git/ampliconPipeLine/plots.R + +fq1=$1 +fq2=$2 +output=$3 + +if [ ! -e $fq1.trim ] +then +echo `date` " [$$] - $adapt_clipper -a $illmP5 $fq1 > $fq1.trim" +$adapt_clipper -a $illmP5 $fq1 > $fq1.trim +echo `date` " [$$] - Done!" +fi + +if [ ! -e $fq1.qtrim ] +then +echo `date` " [$$] - $qTrim -t30 -i $fq1.trim -o $fq1.qtrim -Q34" +$qTrim -t30 -i $fq1.trim -o $fq1.qtrim -Q34 +echo `date` " [$$] - Done!" +fi + +if [ ! -e $fq2.trim ] +then +echo `date` " [$$] - $adapt_clipper -a $illmP7 $fq2 > $fq2.trim" +$adapt_clipper -a $illmP7 $fq2 > $fq2.trim +echo `date` " [$$] - Done!" +fi + +if [ ! -e $fq2.qtrim ] +then +echo `date` " [$$] - $qTrim -t30 -i $fq2.trim -o $fq2.qtrim -Q34" +$qTrim -t30 -i $fq2.trim -o $fq2.qtrim -Q34 +echo `date` " [$$] - Done!" +fi + +if [ ! -e $fq1.qtrim.paired ] +then +echo `date` " [$$] - perl $pairUp $fq1.qtrim $fq2.qtrim" +perl $pairUp $fq1.qtrim $fq2.qtrim +echo `date` " [$$] - Done!" +fi + +if [ ! -e $output ] +then +echo `date` " [$$] - $stampy -g $index -h $hash --bwaoptions=\"$bwaref\" -o $output -M $fq1.qtrim.paired $fq2.qtrim.paired" +$stampy -g $index -h $hash --bwaoptions="$bwaref" -o $output -M $fq1.qtrim.paired $fq2.qtrim.paired +echo `date` " [$$] - Done!" +fi + +if [ ! -e $output.bam ] +then +echo `date` " [$$] - $samtools view -uS $output | $samtools sort - $output" +$samtools view -uS $output | $samtools sort - $output +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $samtools index $output.bam" +$samtools index $output.bam +echo `date` " [$$] - Done!" +fi + +if [ ! -e $output.vcf ] +then +echo `date` " [$$] - $samtools mpileup -Euf $bwaref -L 1000000 -d 1000000 -F 0.01 -m 10 -o 20 $output.bam | bcftools view -bvcg - > $output.bcf" +$samtools mpileup -Euf $bwaref -L 1000000 -d 1000000 -F 0.01 -m 10 -o 20 $output.bam | bcftools view -bvcg - > $output.bcf +echo `date` " [$$] - Done!" +echo `date` " [$$] - bcftools view $output.bcf > $output.vcf" +bcftools view $output.bcf > $output.vcf +echo `date` " [$$] - Done!" +fi + +if [ ! -e $output.txt ] +then +echo `date` " [$$] - java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o txt -c $snpEff/snpEff.config $output.vcf > $output.snpeff.vcf" +java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o txt -c $snpEff/snpEff.config $output.vcf > $output.snpeff.vcf +echo `date` " [$$] - Done!" + +dbSnp=/scratch/data/ref/dbSNP/dbSnp_120616.vcf +dbNSFP=/scratch/data/ref/dbNSFP/dbNSFP2.0b3.txt +snpSift=/opt/SnpSift + +echo `date` " [$$] [$$] - java -jar /opt/SnpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" +java -jar /opt/SnpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf +echo `date` " [$$] [$$] - Done!" + +echo `date` " [$$] [$$] - java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" +java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf +echo `date` " [$$] [$$] - Done!" + +fi + +if [ ! -e $output.qc.txt ] +then +echo `date` " [$$] - $pileup2cov $bwaref $output.bam > $output.qc.txt" +$samtools view -Xq10 $output.bam | $pileup2cov $bwaref > $output.qc.txt +echo `date` " [$$] - Done!" +fi + +if [ ! -e $output.qc.ann.txt ] +then +echo `date` " [$$] - $attachManifest $manifest $output.qc.txt $output.qc.targets.txt > $output.qc.ann.txt" +$attachManifest $manifest $output.qc.txt $output.qc.targets.txt > $output.qc.ann.txt +echo `date` " [$$] - Done!" +fi + +if [ ! -e $output.pdf ] +then +echo `date` " [$$] - $plots $output.qc.ann.targets.txt $output.qc.targets.txt" +$plots $output.qc.ann.txt $output.qc.targets.txt $output.pdf +echo `date` " [$$] - Done!" +fi diff -r 1b81dd6b68b5 -r 9285f791716d falco/amplicon-AlVcAn-TSACP.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/amplicon-AlVcAn-TSACP.sh Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,236 @@ +#!/bin/bash + +DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" +TMP=./tmp +if [ ! -e $TMP ] +then + mkdir $TMP +fi + +index=$DIR/ref/hg19/stampy/hg19 +hash=$DIR/ref/hg19/stampy/hg19 +bwaref=$DIR/ref/hg19/bwa-5/hg19.fa +manifest=$DIR/ref/manifests/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt + +illmP5="AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" +illmP7="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT" + +adapt_clipper=$DIR/bin/cutadapt/cutadapt-1.1/bin/cutadapt +qTrim=$DIR/bin/fastq_quality_trimmer +stampy=$DIR/bin/stampy/stampy-1.0.18/stampy.py +samtools=$DIR/bin/samtools/samtools-0.1.18/samtools +snpEff=$DIR/bin/snpEff/snpEff_3_0a +varscan=$DIR/bin/VarScan/VarScan.v2.2.11.jar +java=/usr/java/latest/bin/java +bwa=$DIR/bin/bwa/bwa-0.5.9/bwa + +pairUp=$DIR/misc/pairUp.pl +pileup2cov=$DIR/misc/pileup2cov.pl +attachManifest=$DIR/misc/attachManifest.pl +plots=$DIR/misc/plots.R +VcAn=$DIR/amplicon-VcAn-TSACP.sh +report=$DIR/amplicon-Report.sh + +fq1=$1 +fq2=$2 +output=$3 + +bfq1=`basename $fq1` +bfq2=`basename $fq2` + +if [ ! -e $TMP/$bfq1.trim ] +then +echo `date` " [$$] - $adapt_clipper -a $illmP5 $fq1 > $TMP/$bfq1.trim" +$adapt_clipper -a $illmP5 $fq1 > $TMP/$bfq1.trim +echo `date` " [$$] - Done!" +fi + +if [ ! -e $TMP/$bfq1.qtrim ] +then +echo `date` " [$$] - $qTrim -t30 -i $TMP/$bfq1.trim -o $TMP/$bfq1.qtrim -Q34" +$qTrim -t30 -i $TMP/$bfq1.trim -o $TMP/$bfq1.qtrim -Q34 +echo `date` " [$$] - Done!" +fi + +if [ ! -e $TMP/$bfq2.trim ] +then +echo `date` " [$$] - $adapt_clipper -a $illmP7 $fq2 > $TMP/$bfq2.trim" +$adapt_clipper -a $illmP7 $fq2 > $TMP/$bfq2.trim +echo `date` " [$$] - Done!" +fi + +if [ ! -e $TMP/$bfq2.qtrim ] +then +echo `date` " [$$] - $qTrim -t10 -i $TMP/$bfq2.trim -o $TMP/$bfq2.qtrim -Q34" +$qTrim -t30 -i $TMP/$bfq2.trim -o $TMP/$bfq2.qtrim -Q34 +echo `date` " [$$] - Done!" +fi + +if [ ! -e $TMP/$bfq1.qtrim.paired ] +then +echo `date` " [$$] - perl $pairUp $TMP/$bfq1.qtrim $TMP/$bfq2.qtrim" +perl $pairUp $TMP/$bfq1.qtrim $TMP/$bfq2.qtrim +echo `date` " [$$] - Done!" +fi + +if [ ! -e $TMP/$output ] +then +echo `date` " [$$] - $stampy -g $index -h $hash --readgroup=ID:$output,SM:$output --gatkcigarworkaround --bwaoptions=\"$bwaref\" --bwa="$bwa" --bwamark -o $TMP/$output -M $TMP/$bfq1.qtrim.paired $TMP/$bfq2.qtrim.paired" +$stampy -g $index -h $hash --readgroup=ID:$output,SM:$output --gatkcigarworkaround --bwaoptions="$bwaref" --bwa="$bwa" --bwamark -o $TMP/$output -M $TMP/$bfq1.qtrim.paired $TMP/$bfq2.qtrim.paired +echo `date` " [$$] - Done!" +fi + +if [ ! -e $output.bam ] +then +echo `date` " [$$] - $samtools view -uS $TMP/$output | $samtools sort - $output" +$samtools view -uS $TMP/$output | $samtools sort - $output +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $samtools index $output.bam" +$samtools index $output.bam +echo `date` " [$$] - Done!" +fi + +echo `date` "[$$] - $VcAn $output.bam $output" +$VcAn $output.bam $output +echo `date` "[$$] - Done!" + +echo `date` "[$$] - $report $output" +$report $output +echo `date` "[$$] - Done!" + +exit +if [ ! -e $output.vcf ] +then +# Use Extended BAQ! +# Tweak indel settings -m and -F +echo `date` " [$$] - $samtools mpileup -Euf $bwaref -L 1000000 -d 1000000 -m 150 -F 0.01 -o 20 $output.bam | bcftools view -bvcg - > $output.bcf" +$samtools mpileup -Euf $bwaref -L 1000000 -d 1000000 -m 150 -F 0.01 -o 20 $output.bam | bcftools view -bvcg - > $output.bcf +echo `date` " [$$] - Done!" +echo `date` " [$$] - bcftools view $output.bcf > $output.vcf" +bcftools view $output.bcf > $output.vcf +echo `date` " [$$] - Done!" +fi + +if [ ! -e $output.vs.snp.vcf ] +then +# VarScan seems a better alternative for smaller VAF's Samtools seems to obscure some false negatives.... +echo `date` " [$$] - $samtools mpileup -Bf $bwaref $output.bam | $java -jar $varscan mpileup2snp --min-var-freq 0.05 --output-vcf > $output.vs.snp.vcf" +$samtools mpileup -Bf $bwaref $output.bam | $java -jar $varscan mpileup2snp --min-var-freq 0.05 --output-vcf > $output.vs.snp.vcf +echo `date` " [$$] - Done!" +fi + +if [ ! -e $output.vs.snp.tsv ] +then +# VarScan seems a better alternative for smaller VAF's Samtools seems to obscure some false negatives.... +echo `date` " [$$] - $samtools mpileup -Bf $bwaref $output.bam | $java -jar $varscan mpileup2snp --min-var-freq 0.05 > $output.vs.snp.tsv" +$samtools mpileup -Bf $bwaref $output.bam | $java -jar $varscan mpileup2snp --min-var-freq 0.05 > $output.vs.snp.tsv +echo `date` " [$$] - Done!" +fi + +if [ ! -e $output.vs.indel.vcf ] +then +echo `date` " [$$] - $samtools mpileup -Bf $bwaref $output.bam | $java -jar $varscan mpileup2indel --min-var-freq 0.05 --output-vcf > $output.vs.indel.vcf" +$samtools mpileup -Bf $bwaref $output.bam | $java -jar $varscan mpileup2indel --min-var-freq 0.05 --output-vcf > $output.vs.indel.vcf +echo `date` " [$$] - Done!" +fi + +# Annotation +dbSnp=/scratch/data/ref/dbSNP/dbSnp_120616.vcf +dbNSFP=/scratch/data/ref/dbNSFP/dbNSFP2.0b3.txt +snpSift=/opt/SnpSift + +VcfIn=$output.vcf +VcfOut=$output.samtools.vcf + +if [ ! -e $VcfOut ] +then +# Samtools annotation +echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" +$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf +mv $output.snpeff.vcf $VcfOut +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" +#$java -jar /opt/SnpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" +#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf +#mv $output.snpeff.3.vcf $VcfOut +echo `date` " [$$] - Done!" +fi + +VcfIn=$output.vs.snp.vcf +VcfOut=$output.vs.snp.a.vcf + +if [ ! -e $VcfOut ] +then +# VarScan SNP annotation +echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" +$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf +mv $output.snpeff.vcf $VcfOut +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" +#$java -jar /opt/SnpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" +#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf +#mv $output.snpeff.3.vcf $VcfOut +echo `date` " [$$] - Done!" +fi + +VcfIn=$output.vs.indel.vcf +VcfOut=$output.vs.indel.a.vcf + +if [ ! -e $VcfOut ] +then +# VarScan INDEL annotation +echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" +$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf +mv $output.snpeff.vcf $VcfOut +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" +#$java -jar /opt/SnpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" +#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf +#mv $output.snpeff.3.vcf $VcfOut +echo `date` " [$$] - Done!" +fi + + +if [ ! -e $output.qc.txt ] +then +echo `date` " [$$] - $pileup2cov $bwaref $output.bam > $output.qc.txt" +$samtools view -Xq10 $output.bam | $pileup2cov $bwaref > $output.qc.txt +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $samtools view -Xq10 -f0x0040 $output.bam | $pileup2cov $bwaref $output.bam > $output.R1.qc.txt" +$samtools view -Xq10 -f0x0040 $output.bam | $pileup2cov $bwaref > $output.R1.qc.txt +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $samtools view -Xq10 -f0x0080 $output.bam | $pileup2cov $bwaref $output.bam > $output.R2.qc.txt" +$samtools view -Xq10 -f0x0080 $output.bam | $pileup2cov $bwaref > $output.R2.qc.txt +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $attachManifest $manifest $output.qc.txt $output.qc.targets.txt > $output.qc.ann.txt" +$attachManifest $manifest $output.qc.txt $output.qc.targets.txt > $output.qc.ann.txt +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $attachManifest $manifest $output.R1.qc.txt $output.R1.qc.targets.txt > $output.R1.qc.ann.txt" +$attachManifest $manifest $output.R1.qc.txt $output.R1.qc.targets.txt > $output.R1.qc.ann.txt +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $attachManifest $manifest $output.R2.qc.txt $output.R2.qc.targets.txt > $output.R2.qc.ann.txt" +$attachManifest $manifest $output.R2.qc.txt $output.R2.qc.targets.txt > $output.R2.qc.ann.txt +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $plots $output.qc.ann.targets.txt $output.qc.targets.txt" +$plots $output.qc.ann.txt $output.qc.targets.txt $output.pdf +echo `date` " [$$] - Done!" +fi diff -r 1b81dd6b68b5 -r 9285f791716d falco/amplicon-QC.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/amplicon-QC.sh Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,33 @@ +#!/bin/bash + +bam=$1 +DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" +TMP=./tmp +if [ ! -e $TMP ] +then + mkdir $TMP +fi + +source $DIR/init.sh + +#targetBed=$DIR/ref/manifests/TSACP/TSACP.bed +#samtools=$DIR/bin/samtools/samtools-0.1.18/samtools +#alignmentStats=$DIR/misc/alignmentStats.pl +#errorRate=$DIR/misc/errorRate.pl +#plotQc=$DIR/misc/plotsQC.R + +#export PATH=$PATH:$DIR/bin/samtools/samtools-0.1.18/ + +if [ ! -e alignmentStats.tsv ] +then +$alignmentStats $targetBed $bam > alignmentStats.tsv +fi + +if [ ! -e errorStats.tsv ] +then +$errorRate *.qc.ann.txt > errorStats.tsv +fi + +Rscript $plotQc alignmentStats.tsv errorStats.tsv + + diff -r 1b81dd6b68b5 -r 9285f791716d falco/amplicon-Report.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/amplicon-Report.sh Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,44 @@ +#!/bin/bash + +DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" + +source $DIR/init.sh + + +base=$1 + +vcf2tsv=$DIR/misc/vcf2tsv.pl +spliteff=$DIR/misc/splitEff.pl +addQc=$DIR/misc/addQc.pl +filterR=$DIR/misc/filter.R +filter=$DIR/misc/filter.pl +plotPng=$DIR/misc/plotsPng.R + +# convert to tsv + +echo `date` " [$$] - converting vcf to tsv" +$vcf2tsv $base.samtools.vcf > $base.samtools.tsv +#$vcf2tsv $base.vs.snp.a.vcf > $base.vs.snp.a.tsv +$vcf2tsv $base.qc.ann.filt.a.vcf > $base.qc.ann.filt.a.tsv +$vcf2tsv $base.qc.ann.clinvar.a.vcf > $base.qc.ann.clinvar.a.tsv +#$vcf2tsv $base.qc.ann.2.a.vcf > $base.qc.ann.2.a.tsv + +# split eff columns +echo `date` " [$$] - splitting vcf columns" +$spliteff $base.samtools.tsv Samtools > $base.res.tsv +#$spliteff $base.vs.snp.a.tsv >> $base.res.tsv +$spliteff $base.qc.ann.filt.a.tsv Custom >> $base.res.tsv +$spliteff $base.qc.ann.clinvar.a.tsv Clinvar >> $base.res.tsv +#$spliteff $base.qc.ann.2.a.tsv Custom2 >> $base.res.tsv + +# add count data +#$addQc $base.res.tmp $base.qc.ann.txt > $base.res.tsv + +# Filter +echo `date` " [$$] - filtering data" +#Rscript $filterR $base.res.tsv $base.qc.ann.txt 10 100 .95 $base +$filter $base.res.tsv $canonicals > $base.res.filtered.tsv + +# Plot +echo `date` " [$$] - plotting data" +Rscript $plotPng $base.qc.ann.qual.txt $base.qc2.ann.txt $base.qc.targets.txt $base.res.filtered.tsv $base.qc.ann.qual.clinvar.txt $locifilt $base diff -r 1b81dd6b68b5 -r 9285f791716d falco/amplicon-VcAn-TSACP.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/amplicon-VcAn-TSACP.sh Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,120 @@ +#!/bin/bash + +DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" + +source $DIR/init.sh + +TMP=./tmp +if [ ! -e $TMP ] +then + mkdir $TMP +fi + +bam=$1 +output=$2 + +if [ ! -e $output.vcf ] +then +# Use Extended BAQ! +# Tweak indel settings -m and -F +echo `date` " [$$] - $samtools mpileup -Euf $faref -L 1000000 -d 1000000 -m 150 -F 0.01 -o 20 $bam | bcftools view -bvcg - > $output.bcf" +$samtools mpileup -Euf $faref -L 1000000 -d 1000000 -m 150 -F 0.01 -o 20 $bam | $bcftools view -bvcg - > $output.bcf +echo `date` " [$$] - Done!" +echo `date` " [$$] - bcftools view $output.bcf > $output.vcf" +$bcftools view $output.bcf > $output.vcf +echo `date` " [$$] - Done!" +fi + +# Annotation +VcfIn=$output.vcf +VcfOut=$output.samtools.vcf + +if [ ! -e $VcfOut ] +then +# Samtools annotation +echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" +$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" +$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf +mv $output.snpeff.2.vcf $VcfOut +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" +#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf +#mv $output.snpeff.3.vcf $VcfOut +echo `date` " [$$] - Done!" +fi + +if [ ! -e $output.qc.ann.txt ] +then +echo `date` " [$$] - $pileup2cov2 $bam $faref $manifest $output $samtools" +$pileup2cov2 $bam $faref $manifest $output $samtools +echo `date` " [$$] - Done!" +fi + +if [ ! -e $output.qc.ann.qual.txt ] +then +echo `date` " [$$] - RScript $addQual $output.qc.ann.txt $output.qc.ann.qual.txt $DIR/misc/func.R $locifilt" +Rscript $addQual $output.qc.ann.txt $output.qc.ann.qual.txt $DIR/misc/func.R $locifilt +echo `date` " [$$] - Done!" +fi + +echo `date` " [$$] - $qcFilt $output.qc.ann.qual.txt $clinvar $cosmic $cosmicNC $output" +$qcFilt $output.qc.ann.qual.txt $clinvar $cosmic $cosmicNC $output +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $qc2vcf $output.qc.ann.qual.filt.txt > $output.qc.ann.filt.vcf" +$qc2vcf $output.qc.ann.qual.filt.txt > $output.qc.ann.filt.vcf +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $qc2vcf $output.qc.ann.qual.clinvar.txt > $output.qc.ann.clinvar.vcf" +$qc2vcf $output.qc.ann.qual.clinvar.txt > $output.qc.ann.clinvar.vcf +echo `date` " [$$] - Done!" + + + +VcfIn=$output.qc.ann.filt.vcf +VcfOut=$output.qc.ann.filt.a.vcf + +if [ ! -e $VcfOut ] +then + +# qc vcf annotation +echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" +$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" +$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf +mv $output.snpeff.2.vcf $VcfOut +echo `date` " [$$] - Done!" + +#echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" +#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf +#mv $output.snpeff.3.vcf $VcfOut +#echo `date` " [$$] - Done!" +fi + +VcfIn=$output.qc.ann.clinvar.vcf +VcfOut=$output.qc.ann.clinvar.a.vcf + +if [ ! -e $VcfOut ] +then + +# qc vcf annotation +echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" +$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf +echo `date` " [$$] - Done!" + +echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" +$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf +mv $output.snpeff.2.vcf $VcfOut +echo `date` " [$$] - Done!" + +#echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" +#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf +#mv $output.snpeff.3.vcf $VcfOut +#echo `date` " [$$] - Done!" +fi diff -r 1b81dd6b68b5 -r 9285f791716d falco/bin/fastq_quality_trimmer Binary file falco/bin/fastq_quality_trimmer has changed diff -r 1b81dd6b68b5 -r 9285f791716d falco/init.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/init.sh Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,57 @@ +#!/bin/bash + +DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" + +index=/ccagc/data/ref/hg19/stampy/hg19 +hash=/ccagc/data/ref/hg19/stampy/hg19 +faref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa +bwaref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa +manifest=/ccagc/data/ref/manifests/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt +targetBed=/ccagc/data/ref/manifests/TSACP/TSACP.bed + +dbSnp=/ccagc/data/ref/dbSNP/common_no_known_medical_impact_00-latest.f.vcf +dbNSFP=/ccagc/data/ref/dbNSFP/dbNSFP2.0b3.txt +clinvar=/ccagc/data/ref/dbSNP/clinvar_00-latest.f.vcf +cosmic=/ccagc/data/ref/cosmic/CosmicCodingMuts_v64_26032013_noLimit_wgs.f.vcf +cosmicNC=/ccagc/data/ref/cosmic/CosmicNonCodingVariants_v64_26032013_noLimit_wgs.f.vcf +locifilt=/ccagc/data/ref/dbSNP/locifilt.tsv +canonicals=/ccagc/data/ref/manifests/TSACP/canonicals.tsv + +illmP5="AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" +illmP7="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT" + +adapt_clipper=/ccagc/lib/cutadapt/cutadapt-1.1/bin/cutadapt +qTrim=/ccagc/bin/fastq_quality_trimmer +stampy=/ccagc/lib/stampy/stampy-1.0.18/stampy.py +samtools=/ccagc/lib/samtools/samtools-0.1.18/samtools +bcftools=/ccagc/lib/samtools/samtools-0.1.18/bcftools/bcftools +#snpEff=/ccagc/lib/snpEff/snpEff_3_0a +snpEff=/ccagc/lib/snpEff/snpEff_v3_4 +snpSift=/ccagc/lib/SnpSift + +varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar +java=/usr/bin/java +bwa=/ccagc/lib/bwa/bwa-0.5.9/bwa +flash=/ccagc/lib/flash/FLASH-1.2.2/flash + +pairUp=$DIR/misc/pairUp.pl +pileup2cov=$DIR/misc/pileup2cov.pl +pileup2cov2=$DIR/misc/perAmpliconAnalysis.pl +addQual=$DIR/misc/addQual.R + +qc2vcf=$DIR/misc/qc2vcf.pl +qcFilt=$DIR/misc/qcFilt.pl +plots=$DIR/misc/plots.R +plotsPng=$DIR/misc/plotsPng.R + +attachManifest=$DIR/misc/attachManifest.pl +plots=$DIR/misc/plots.R +VcAn=$DIR/amplicon-VcAn-TSACP.sh +report=$DIR/amplicon-Report.sh + +alignmentStats=$DIR/misc/alignmentStats.pl +errorRate=$DIR/misc/errorRate.pl +plotQc=$DIR/misc/plotsQC.R + +export PATH=$PATH:/ccagc/lib/samtools/samtools-0.1.18/ +source ./galaxy_init.sh diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/addQc.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/addQc.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,74 @@ +#!/usr/bin/perl + +use strict; + +my $file = shift; +my $qc = shift; +my %crds = (); +open F, "<$file"; +my $fhead = readline F; +chomp $fhead; +print $fhead . "\t" . join("\t", qw/dp dpref dpvar vaf/) . "\n"; +while () { + chomp; + my @row = split(/\t/, $_, -1); +# print STDERR scalar(@row) . "\n"; + push @{$crds{$row[0]}{$row[1]}}, [@row]; +} +close F; + +# INDELS? +my %ntcol = (A => 8, C => 9, G => 10, T => 11); +open QC, "<$qc"; +while () { + chomp; + my @row = split(/\t/, $_); + next if ($row[2] eq "."); + my $muts = $crds{$row[0]}{$row[1]} || undef; + next unless $muts; + foreach my $mut (@$muts) { + my $rl = length($mut->[3]); + my $vl = length($mut->[4]); + + my $refDP = $row[$ntcol{uc($row[4])}]; + + if ($rl > $vl && $row[14] ne ".") { # Deletion + my %dels = split(/[\|\:]/, $row[14]); + my @del = sort { $dels{$b} <=> $dels{$a} } keys(%dels); + my $deldp = $dels{$del[0]}; + print join("\t", @{$mut}, $row[3], $row[6] - $deldp, $deldp, $deldp / $row[3]) . "\n"; + + } + elsif ($rl < $vl && $row[13] ne ".") { # Insertion + my %inss = split(/[\|:]/, $row[13]); + my @ins = sort { $inss{$b} <=> $inss{$a} } keys(%inss); + my $insdp = $inss{$ins[0]}; + print join("\t", @{$mut}, $row[3], $row[6] - $insdp, $insdp, $insdp / $row[3]) . "\n"; + } + elsif ($rl == $vl) { + my @varnts = sort { $row[$ntcol{$b}] <=> $row[$ntcol{$a}] } split(/\//, $row[5]); + next if ($row[$ntcol{$varnts[0]}] == $row[$ntcol{$varnts[1]}]); # Equeal variant counts + my $vardp = $row[$ntcol{$varnts[0]}]; + print join("\t", @{$mut}, $row[3], $row[6], $vardp, $vardp / ($row[6] + $vardp)) . "\n"; + } + + } + next; +# if (exists($crds{$row[0]}{$row[1]}) && length($crds{$row[0]}{$row[1]}->[3]) > 1) { # In case of snp + if (exists($crds{$row[0]}{$row[1]})) { # && length($crds{$row[0]}{$row[1]}->[3]) > 1) { # In case of snp + print join("\t", @{$_}, $row[3], $row[6], $row[7], $row[7] / $row[3]) . "\n" foreach @{$crds{$row[0]}{$row[1]}}; + } + if ($row[14] ne "." && exists($crds{$row[0]}{$row[1]})) { # In case of deletion! + my %dels = split(/[\|\:]/, $row[14]); + my @del = sort { $dels{$b} <=> $dels{$a} } keys(%dels); + $row[7] = $dels{$del[0]}; + print join("\t", @{$_}, $row[3], $row[6] - $row[7], $row[7], $row[7] / $row[3]) . "\n" foreach @{$crds{$row[0]}{$row[1]}}; + } + if ($row[13] ne "." && exists($crds{$row[0]}{$row[1]})) { # In case of insertion + my %inss = split(/[\|:]/, $row[13]); + my @ins = sort { $inss{$b} <=> $inss{$a} } keys(%inss); + $row[7] = $inss{$ins[0]}; + print join("\t", @{$_}, $row[3], $row[6] - $row[7], $row[7], $row[7] / $row[3]) . "\n" foreach @{$crds{$row[0]}{$row[1]}}; + } +} +close QC; diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/addQual.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/addQual.R Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,21 @@ +#!/usr/bin/Rscript +args <- commandArgs(T) +qcFile <- args[1] +output <- args[2] +funcR <- args[3] +lociFiltFile <- args[4] + +read.delim(lociFiltFile, header=F) -> lociFiltD +lociFilt <- paste(paste("chr", lociFiltD[,1], sep=""), lociFiltD[,2], sep=":") + +source(funcR) +read.delim(qcFile, header=T) -> qc + +#addQual(qc) -> qc.qual +addQualTransCor(qc, lociFilt) -> qc.qual +#addQualVarCor(qc) -> qc.qual + +write.table(qc.qual, output, row.names=F, col.names=T, quote=F, sep="\t") +#write.table(qc[selection,], output, row.names=F, col.names=T, quote=F, sep="\t") + + diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/alignmentStats.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/alignmentStats.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,69 @@ +#!/usr/bin/perl -w + +use strict; + +my $targetBed = shift; +my @bams = @ARGV; +$|= 1; + +foreach my $bam (@bams) { + my $file = `basename $bam`; + chomp $file; + my $res0 = `samtools idxstats $bam`; + my @Qdat = (); + my %Q = (); + my $mapped = 0; + my $ontarget = 0; + my $unmapped = 0; + while ($res0 =~ /(\S+)\s(\S+)\s(\S+)\s(\S+)\n/g) { + if ($1 ne "*") { + $mapped += $3; + $unmapped += $4; + } + else { + $unmapped += $3; + $unmapped += $4; + } + } + my %Qcon = map { chr($_ + 33) => $_ } (0 .. 40); + open PIPE, "samtools view -XF0x014 -L $targetBed $bam | cut -f11 |"; + while () { + my @is = (0 .. (length($_) - 2)); + $ontarget++; + foreach my $i (@is) { + $Qdat[$i][$Qcon{substr($_, $i, 1)}]++; + } + } + + open PIPE, "samtools view -XF0x004 -f0x010 -L $targetBed $bam | cut -f11 |"; + while () { + my @is = reverse(0 .. (length($_) - 2)); + $ontarget++; + foreach my $i (@is) { + $Qdat[$i][$Qcon{substr($_, $i, 1)}]++; + } + } + + open QUAL, ">$file.qual.tsv"; + print QUAL join("\t", "pos", 0 .. $#Qdat) . "\n"; + my $q0 = 0; + my $q10 = 0; + my $q20 = 0; + my $q30 = 0; + my $qtot = 0; + foreach my $p (0 .. $#Qdat) { + print QUAL join("\t", $p, map { $Qdat[$p][$_] || 0 } (0 .. $#{$Qdat[$p]})) . "\n"; + foreach my $q (0 .. $#{$Qdat[$p]}) { + $qtot += $Qdat[$p][$q] || 0; + $q30 += $Qdat[$p][$q] || 0 if ($q >= 30); + $q20 += $Qdat[$p][$q] || 0 if ($q >= 20 && $q < 30); + $q10 += $Qdat[$p][$q] || 0 if ($q >= 10 && $q < 20); + $q0 += $Qdat[$p][$q] || 0 if ($q < 10); + } + } + close QUAL; + + my $offtarget = $mapped - $ontarget; + print join("\t", $file, $mapped, $ontarget, $offtarget, $unmapped, $q30/$qtot, $q20/$qtot, $q10/$qtot, $q0/$qtot) . "\n"; + +} diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/attachGff.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/attachGff.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,69 @@ +#!/usr/bin/perl -w +# +# TODO: tiled targets give wrong length... +use strict; + +my $gff = shift; +my $covtable = shift; + +my $QCrep = shift || "qc.txt"; + +my %targets = (); +my %stats = (); +my %manif = (); +open M, "<$gff"; +while () { + if (/^track/) { + my $h = readline M; + chomp $h; + my @H = split(/\t/, $h); +# print $_ . ":" . $H[$_] . "\n" foreach (0 .. $#H); + last; + } +} +while () { + chomp; + s/\s+$//; + my @row = split(/\t/, $_); + push @{$targets{$row[0]}{$_}}, $row[8] foreach ($row[3] .. $row[4]); + $manif{$row[8]} = [@row]; + if (not exists($stats{$row[8]}{dat})) { + $stats{$row[8]}{dat} = [@row]; + $stats{$row[8]}{ln} = $row[4] - $row[3] + 1; + $stats{$row[8]}{n} = 0; + $stats{$row[8]}{covs} = []; + } +} +close M; + +open C, "<$covtable"; +while () { + chomp; + my @row = split(/\t/, $_); + $#row = 13; + if (exists($targets{$row[0]}{$row[1]})) { + foreach my $t (@{$targets{$row[0]}{$row[1]}}) { + $stats{$t}{n}++; + $stats{$t}{covSum} += $row[2]; + push @{$stats{$t}{covs}}, $row[2]; + } + } + print join("\t", @row[0 .. 1], + (join("|", @{$targets{$row[0]}{$row[1]} || ["."]} )), + (@row[2 .. 11]), + (map { $_ || "." } @row[12 .. $#row]), + ). "\n"; +# sleep 1; +} +close C; + +# Calc assay stats +open QC, ">$QCrep"; +foreach my $t (sort keys %stats) { + my @covs = sort {$a <=> $b} @{$stats{$t}{covs}}; + my $mean = ($stats{$t}{n} != 0)?$stats{$t}{covSum} / $stats{$t}{n}:0; + #print join("\t", @{$stats{$t}{dat}}, $mean, map { $stats{$t}{$_} } qw/ln n/). "\n"; + print QC join("\t", $t, sprintf("%.2f", $mean), map { $stats{$t}{$_} } qw/ln n/). "\n"; + +} +close QC; diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/attachManifest.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/attachManifest.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,83 @@ +#!/usr/bin/perl -w +# +# TODO: tiled targets give wrong length... +use strict; + +my $manifest = shift; +my $covtable = shift; + +my $QCrep = shift || "qc.txt"; + +my %targets = (); +my %stats = (); +my %manif = (); +open M, "<$manifest"; +while () { last if (/\[Probes\]/) } +readline(M); +while () { + chomp; + if (/\[Targets\]/) { + my $h = readline M; + chomp $h; + my @H = split(/\t/, $h); +# print $_ . ":" . $H[$_] . "\n" foreach (0 .. $#H); + last; + } + my @row = split(/\t/, $_); + $stats{$row[2]}{probe} = [@row]; + $stats{$row[2]}{ULSO} = $row[9]; + $stats{$row[2]}{DLSO} = $row[11]; + + +} +while () { + chomp; + s/\s+$//; + my @row = split(/\t/, $_); + push @{$targets{$row[3]}{$_}}, $row[0] foreach ($row[4] .. $row[5]); + $manif{$row[0]} = [@row]; + if (not exists($stats{$row[0]}{target})) { + $stats{$row[0]}{target} = [@row]; + $stats{$row[0]}{ln} = $row[5] - $row[4] + 1; + $stats{$row[0]}{n} = 0; + $stats{$row[0]}{covs} = []; + $stats{$row[0]}{chr} = $row[3]; + $stats{$row[0]}{start} = $row[4]; + $stats{$row[0]}{end} = $row[5]; + $stats{$row[0]}{assayStart} = $row[4] + length($stats{$row[0]}{ULSO}); + $stats{$row[0]}{assayEnd} = $row[5] - length($stats{$row[0]}{DLSO}); + } +} +close M; + +open C, "<$covtable"; +while () { + chomp; + my @row = split(/\t/, $_); + $#row = 13; + if (exists($targets{$row[0]}{$row[1]})) { + foreach my $t (@{$targets{$row[0]}{$row[1]}}) { + $stats{$t}{n}++; + $stats{$t}{covSum} += $row[2]; + push @{$stats{$t}{covs}}, $row[2]; + } + } + print join("\t", @row[0 .. 1], + (join("|", @{$targets{$row[0]}{$row[1]} || ["."]} )), + (@row[2 .. 11]), + (map { $_ || "." } @row[12 .. $#row]), + ). "\n"; +# sleep 1; +} +close C; + +# Calc assay stats +open QC, ">$QCrep"; +foreach my $t (sort keys %stats) { + my @covs = sort {$a <=> $b} @{$stats{$t}{covs} || []}; + my $mean = ($stats{$t}{n} != 0)?$stats{$t}{covSum} / $stats{$t}{n}:0; + #print join("\t", @{$stats{$t}{dat}}, $mean, map { $stats{$t}{$_} } qw/ln n/). "\n"; + print QC join("\t", $t, sprintf("%.2f", $mean), map { $stats{$t}{$_} } qw/ln n chr start end assayStart assayEnd/). "\n"; + +} +close QC; diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/checkRunComplete.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/checkRunComplete.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,61 @@ +#!/usr/bin/perl + +use strict; + +# Check RTAcomplete.txt +# Check existence in AnalisysOutput + +my $base = "/ccagc/lib/pipelines/TSACP/falco/misc"; +my $getData = "$base/getData.pl"; +my $startAn = "$base/startAnalysis.pl"; + +my $Project = shift or die "No project specified!\n"; +my $AnalysisOutput = shift || "./"; #"/ccagc/data/SeqAnalysis/$Project"; + +my $MiSeqOutput = shift || "/ccagc/data/processing/MiSeqOutput/"; + + +my $LOG = shift || "$AnalysisOutput/log/$Project.log"; + +if (! -d "$AnalysisOutput/log") { + mkdir "$AnalysisOutput/log"; +} + +my %log = (); +open LOG, "<$LOG"; +while () { + chomp; + # runDir date + my @row = split(/\t/, $_); + $log{$row[0]} = [@row]; +} +close LOG; + +my @runs = `find $MiSeqOutput -maxdepth 2 -iname "RTAComplete.txt"`; +my %runHsh = (); + +foreach my $r (@runs) { + chomp; + my $runDir = `dirname $r`; + chomp $runDir; + if (exists($log{$runDir})) { + print STDERR "$runDir previously checked\n"; + next; + } + my @row = split(/\//, $runDir); + my @run = split(/\_/, $row[$#row]); + my $outDir = $AnalysisOutput . "/" . join("_", @run[0 .. 2]); + my $baseDir = $AnalysisOutput; + if (-e $outDir) { + print STDERR "$outDir exists, skipping\n"; + } else { + print STDERR "perl $getData $runDir $Project\n"; + system("perl $getData $runDir $Project $baseDir"); + print STDERR "perl $startAn $outDir\n"; + system("perl $startAn $outDir"); + open LOG, ">>$LOG"; + print LOG join("\t", $runDir, scalar(localtime())) . "\n"; + close LOG; + } +} + diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/errorRate.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/errorRate.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,36 @@ +#!/usr/bin/perl -w +# + +use strict; +my @files = @ARGV; +foreach my $file (@files) { +my $ref = 0; +my $var = 0; + +my $file = shift; + +open F, "<$file"; +my $header = readline F; # Skip header +chomp $header; +my @hrow = split(/\t/, $header); +my $ci = 0; +my %col = (); +$col{$_} = $ci++ foreach (@hrow); + + +while () { + chomp; + my @row = split(/\t/, $_); + #next if ($row[2] eq "."); + #print join("\t", $row[6], $row[7]) . "\n"; sleep 1; + my $ntRef = uc($row[4]); + $ref += $row[$col{"n$ntRef"}]; + $var += $row[$col{"n$_"}] foreach (grep { $_ ne $ntRef } qw/A C G T/); +} + +close F; +my @path = split(/\//, $file); +my $rate = $var / ($ref + $var) * 100; +#print STDERR "$var/$ref -> $rate%\n"; +print "$path[$#path]\t$var\t$ref\t$rate\n"; +} diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/filter.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/filter.R Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,38 @@ +#!/usr/bin/Rscript +args <- commandArgs(T) +resFile <- args[1] +qcFile <- args[2] +varLim <- args[3] +dpLim <- args[4] +quants <- args[5] +output <- args[6] + +read.delim(resFile, header=T) -> d +read.delim(qcFile, header=T) -> qc + +# Calculate errorrate per amplicon +amps <- unique(qc$X.amp) +for (i in amps) { + sel <- qc$X.amp == amps + prob <- sum(qc$nVar[sel]) / (sum(qc$nRef) + sum(qc$nVar)) + pees <- pbinom(qc$nVar[sel], qc$nRef + qc$nVar, prob, lower.tail=F) + Qscore <- -10 * log10(pees) + +} + +quantile(d$vaf, as.numeric(quants), na.rm=T) -> vafCut + +sel1 <- d$vaf > vafCut +sel2 <- d$dp > dpLim +sel3 <- d$dpvar > varLim + +sel <- sel1 & sel2 & sel3 +write.table(d[sel,], paste(output, "res.f1.tsv", sep="."), row.names=F, col.names=T, quote=F, sep="\t") + +dir.create(output) +setwd(output) + +png(paste(output, "vafcut", "png", sep=".")) +plot(density(log10(d$vaf), na.rm=T), main=paste("VAF cutoff", vafCut, sep=" ")) +abline(v=log10(vafCut), col=2) +dev.off() diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/filter.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/filter.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,100 @@ +#!/usr/bin/perl -w +# + +use strict; + +my $file = shift; +my $canonicals = shift; + +my %can = (); +my %nm = (); + +open CAN, "<$canonicals"; + +while () { + chomp; + my @row = split(/\t/, $_); + $can{$row[0]} = @row[1 .. $#row]; + my $pri = 0; + $nm{$_} = $pri++ foreach @row[1 .. $#row]; +# print STDERR join(":", @row[0,1]) . "\n"; sleep 1; +} + +open F, "<$file"; +my $head = readline(F); +chomp $head; +print $head . "\tvaf\n"; +my @rowHead = split(/\t/, $head); +my $colN = 0; +my %col = map { +# print STDERR $_ . " $colN\n"; + $_ => $colN++ } @rowHead; + +while () { + chomp; + my $line = $_; + my @row = split(/\t/, $_); + #g12 t15 + next unless (exists($can{$row[$col{Gene_Name}]})); + my $trans = $row[$col{Transcript_ID}]; + $trans =~ s/\..*$//; + + if (not exists($nm{$trans})) { + print STDERR "Unknown transcript: $row[$col{Gene_Name}] $trans\n"; + next; + } + elsif ($nm{$trans} != 0) { + print STDERR "Non cannonical: $row[$col{Gene_Name}] $trans\n"; + next; + } + + #next unless ($nm{$trans} == 0); + + # Do not filter out clinicvar loci + #print $_ . "\n" if ($row[$col{Tag}] eq "Clinvar"); + next if ($row[$col{Tag}] eq "Clinvar"); +# print STDERR $row[15]; sleep 1; +# print STDERR $nm{$row[15]}; sleep 1; + +#CODON_CHANGE_PLUS_CODON_DELETION +#CODON_DELETION +#DOWNSTREAM +#EXON +#FRAME_SHIFT +#INTRON +#NON_SYNONYMOUS_CODING +#SPLICE_SITE_ACCEPTOR +#SYNONYMOUS_CODING +#UPSTREAM +#UTR_3_PRIME + + # Filter INTERGENIC + next if ($row[$col{Context}] eq "INTERGENIC"); + + # Filter SYNONYMOUS_CODING + # Dubbel mutatie BRAF +# next if ($row[$col{Context}] eq "SYNONYMOUS_CODING"); + + # Filter INTRON + next if ($row[$col{Context}] eq "INTRON"); + + # Filter dbSNP +# next if ($row[2] ne "."); + + # Filter depth + next if ($row[$col{DP}] < 100); + + my ($nref, $nvar) = split(/,/, $row[$col{AD}]); + # Filter var depth +# print STDERR "DEBUG: " . $nvar . "\n"; sleep 1; + next if ($nvar < 10); + + my $vaf = $nvar / ($nref + $nvar); +# print STDERR "DEBUG: " . $vaf . "\n"; + # Filter vaf + next if ($vaf < 0.01); + + + print $_ . "\t$vaf\n"; +} +close F; diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/filterQC.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/filterQC.R Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,118 @@ +#!/usr/bin/Rscript +args <- commandArgs(T) +qcFile <- args[1] +varLim <- as.numeric(args[2]) +dpLim <- as.numeric(args[3]) +quants <- as.numeric(args[4]) +output <- args[5] + +read.delim(qcFile, header=T) -> d + +vaf <- d$nVar / (d$nRef + d$nVar) + +sapply(1:nrow(d), function(x) { + if (d$del[x] != ".") { + dels <- matrix(unlist(strsplit(as.character(d$del[x]), c("[:|]"))), byrow=T, ncol=2) + delRanks <- rank(dels[,2]) + delDp <- as.numeric(dels[rev(delRanks)[1],2]) + if (delDp > varLim) { + return(T) + } + } + if (d$ins[x] != ".") { + ins <- matrix(unlist(strsplit(as.character(d$ins[x]), c("[:|]"))), byrow=T, ncol=2) + insRanks <- rank(ins[,2]) + insDp <- as.numeric(ins[rev(insRanks)[1],2]) + if (insDp > varLim) { + return(T) + } + + } + return(F) +}) -> indelSel + + +#dels <- matrix(unlist(strsplit(d$del, ":|")) +#inss <- strsplit(d$ins, ":|") +#d$vafDel +#d$vafIns + +quantile(vaf, as.numeric(quants), na.rm=T) -> vafCut + +sel1 <- vaf > vafCut +sel2 <- d$dp > dpLim +sel3 <- (d$nVar > varLim) | indelSel + +sel <- sel1 & sel2 & sel3 +write.table(d[sel,], paste(output, "res.sigfilt.tsv", sep="."), row.names=F, col.names=F, quote=F, sep="\t") + +dir.create(output) +setwd(output) + +png(paste(output, "vafcut", "png", sep=".")) +plot(density(log10(vaf), na.rm=T), main=paste("VAF cutoff", vafCut, sep=" ")) +abline(v=log10(vafCut), col=2) +dev.off() + +ampls <- unique(d$amp) + +pdf(paste(output, "pdf", sep="."), width=14) +sapply(ampls, function(x) { + sel <- d[,3] == x + main = x +# plot(density(as.numeric(as.vector(d[sel,8]))), main=main) +# hist(as.numeric(as.vector(d[sel,8])), breaks=range(d[sel,8])[2], main=main) + + # Get indels + dels <- (d[,15] != ".") & sel + ins <- (d[,14] != ".") & sel + + pNoise <- sum(d$nVar[sel]) / (sum(d$nRef[sel]) + sum(d$nVar[sel])) + print(pNoise) + pVals <- ppois(d$nVar[sel], (d$nVar[sel] + d$nRef[sel]) * pNoise, lower.tail=F) + Qval <- -10*log10(pVals) + noiseThrs <- qpois(0.01, (d$nVar[sel] + d$nRef[sel]) * pNoise) + + plot(d[sel,2], d[sel,4], pch=20, type="s", ylim=c(0, max(d[sel,4])), main=main) + lines(d[sel,2], d[sel,7], pch=20, type="s", col=2) + lines(d[sel,2], d[sel,8], pch=20, type="s",col=3) + + ampMax <- max(d[sel,4]) + + for (idx in which(dels)) { + matrix(unlist(strsplit(as.character(as.vector(d[idx,15])), "[:|]")), ncol=2, byrow=T) -> delDat + nchar(delDat[,1]) -> lngts + dpths <- as.numeric(delDat[,2]) + rect(d[idx,2] + 1, ampMax - dpths , d[idx,2] + lngts, ampMax, col="#00000040") + } + + for (idx in which(ins)) { + matrix(unlist(strsplit(as.character(as.vector(d[idx,14])), "[:|]")), ncol=2, byrow=T) -> insDat + nchar(insDat[,1]) -> lngts + dpths <- as.numeric(insDat[,2]) + for (i in 1:ncol(insDat)) { + polygon( + c(d[idx,2], d[idx,2] - (.5 * lngts[i]), d[idx, 2] + (.5 * lngts[i])), + c(ampMax, ampMax - dpths[i], ampMax - dpths[i]), + , col="#00000040") + } + } + + #abline(v=d[dels,2], col=4) + #abline(v=d[ins,2], col=5) + + vaf <- d[sel,8]/(d[sel,7] + d[sel,8]) + + plot(density(vaf), main=main) + + hist(vaf, breaks=100, main=main) + + plot(d[sel,2], d[sel,8]/(d[sel,7] + d[sel,8]), pch=20, cex=.5, ylim=c(0,1), main=main) + points(d[sel,2], noiseThrs / (d[sel,7] + d[sel,8]), col=2, pch=20) + plot(d[sel,2], log10(d[sel,8]/(d[sel,7] + d[sel,8])), pch=20, cex=.5, ylim=c(-4,0), main=main) + points(d[sel,2], log10(noiseThrs / (d[sel,7] + d[sel,8])), col=2, pch=20) + print(x) +# print(sum(sel)) + }) + +dev.off() diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/func.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/func.R Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,569 @@ +#!/usr/bin/Rscript +#args <- commandArgs(T) +#qcFile <- args[1] +#output <- args[2] + +#read.delim(qcFile, header=T) -> qc + +addQual <- function(qc) { + +qc$del <- as.character(as.vector(qc$del)) +qc$ins <- as.vector(qc$ins) +qc$pVal <- 1 +qc$pValAdj <- 1 +#qc$pValPois <- 1 +qc$qScore <- 0 +qc$qScoreI <- 0 +qc$qScoreD <- 0 + +pVal.I <- rep(1, nrow(qc)) +pVal.D <- rep(1, nrow(qc)) + +delSel <- qc$del != "." +data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[delSel]), "\\|")), ":")), ncol=2, byrow=T)) -> dels +dels$ln <- nchar(as.vector(dels$X1)) +colnames(dels) <- c("seq", "occ", "ln") +delPees <- ppois(1:50, mean(rep(dels$ln, dels$occ)), lower.tail=F) + +insSel <- qc$ins != "." +data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[insSel]), "\\|")), ":")), ncol=2, byrow=T)) -> inss +inss$ln <- nchar(as.vector(inss$X1)) +colnames(inss) <- c("seq", "occ", "ln") +insPees <- ppois(1:50, mean(rep(dels$ln, dels$occ)), lower.tail=F) + +# Calculate errorrate per amplicon +amps <- unique(qc$amp) +for (i in amps) { + print(i) + sel <- qc$amp == i + prob <- sum(qc$nVar[sel]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) + #prob <- median(qc$nVar[sel] / (qc$nRef[sel] + qc$nVar[sel])) + pees <- pbinom(qc$nVar[sel], qc$nRef[sel] + qc$nVar[sel], prob, lower.tail=F) + qc$pVal[sel] <- pees +# pois <- ppois(qc$nVar[sel], (qc$nRef + qc$nVar) * prob, lower.tail=F) +# qc$pValPois[sel] <- pois + + # Seperate for indel/deletion events + selDels <- delSel & sel + if (sum(selDels) > 0) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[selDels]), "\\|")), ":")), ncol=2, byrow=T)) -> dels2 + dels2$ln <- nchar(as.vector(dels2$X1)) + colnames(dels2) <- c("seq", "occ", "ln") + dels2$occ <- as.numeric(as.vector(dels2$occ)) + } + for (j in which(selDels)) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[j]), "\\|")), ":")), ncol=2, byrow=T)) -> dels + dels$ln <- nchar(as.vector(dels$X1)) + colnames(dels) <- c("seq", "occ", "ln") + dels$occ <- as.numeric(as.vector(dels$occ)) + #dels$pDel <- delPees[as.integer(dels$ln)] + #dels$pVal <- ppois(as.numeric(dels$occ), dels$pDel, lower.tail=F) + dels$pDel <- sapply(dels$ln, function(x) {sum(dels2$occ[dels2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) + dels$pVal <- pbinom(dels$occ, qc$dp[j], dels$pDel, lower.tail=F) + dels$Q <- -10 * log10(dels$pVal) + + high <- order(dels$occ, -dels$Q, decreasing=T)[1] + qc$del[j] <- paste(dels$seq[high], dels$occ[high], sep=":") + qc$qScoreD[j] <- dels$Q[high] + pVal.D[j] <- dels$pVal[high] + } + selIns <- insSel & sel + if (sum(selIns) > 0) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[selIns]), "\\|")), ":")), ncol=2, byrow=T)) -> inss2 + inss2$ln <- nchar(as.vector(inss2$X1)) + colnames(inss2) <- c("seq", "occ", "ln") + inss2$occ <- as.numeric(as.vector(inss2$occ)) + } + for (j in which(selIns)) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[j]), "\\|")), ":")), ncol=2, byrow=T)) -> inss + inss$ln <- nchar(as.vector(inss$X1)) + colnames(inss) <- c("seq", "occ", "ln") + inss$occ <- as.numeric(as.vector(inss$occ)) + #inss$pIns <- insPees[as.integer(inss$ln)] + #inss$pVal <- ppois(as.numeric(inss$occ), inss$pIns, lower.tail=F) + inss$pIns <- sapply(inss$ln, function(x) {sum(inss2$occ[inss2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) + inss$pVal <- pbinom(inss$occ, qc$dp[j], inss$pIns, lower.tail=F) + inss$Q <- -10 * log10(inss$pVal) + + high <- order(inss$occ, -inss$Q, decreasing=T)[1] + qc$ins[j] <- paste(inss$seq[high], inss$occ[high], sep=":") + qc$qScoreI[j] <- inss$Q[high] + pVal.I[j] <- inss$pVal[high] + } + print(sum(-10 * log10(pees) > 100)) + print(sum(qc$qScoreI[selIns] > 100)) + print(sum(qc$qScoreD[selDels] > 100)) +} + +p.adjust(qc$pVal) -> qc$pValAdj +-10 * log(p.adjust(pVal.I)) -> qc$qScoreI +-10 * log(p.adjust(pVal.D)) -> qc$qScoreD +qc$qScore <- -10 * log10(qc$pValAdj) +#qc$qScore[qc$pValAdj == 0] <- 1000 +qc$qScore[qc$qScore > 1000] <- 1000 +qc$qScoreI[qc$qScoreI > 1000] <- 1000 +qc$qScoreD[qc$qScoreD > 1000] <- 1000 +qsel <- (qc$qScore >= 100 & qc$nVar >= 10) | (qc$qScoreI >= 200) | (qc$qScoreD >= 200) +dpfilt <- as.numeric(qc$dp) >= 100 +#varfilt <- as.numeric(qc$nVar) >= 10 + +selection <- qsel & dpfilt + +print(paste("Filtered out: ", sum(!selection), sep="")) +print(paste("Variants selected: ", sum(selection), sep="")) +return(qc) +} + +addQualTransCor <- function(qc, lociFilt) { + + +# lociFilt contains snp, cosmic and clinvar positions + +qc$del <- as.character(as.vector(qc$del)) +#qc$del <- as.character(as.vector(qc$del)) +qc$ins <- as.character(as.vector(qc$ins)) +qc$pVal <- 1 +qc$pValAdj <- 1 +#qc$pValPois <- 1 +qc$qScore <- 0 +qc$qScoreI <- 0 +qc$qScoreD <- 0 + +pVal.I <- rep(1, nrow(qc)) +pVal.D <- rep(1, nrow(qc)) + +rle(as.vector(qc$ntRef)) -> srle +hompols <- srle$lengths >= 5 +homPosS <- cumsum(srle$lengths)[hompols] +homPosE <- cumsum(srle$lengths)[which(hompols) - 1] +homFilt <- rep(F, nrow(qc)) +homFilt[homPosS] <- T +homFilt[homPosE] <- T + +delSel <- qc$del != "." & !homFilt +if (sum(delSel > 0)) { + + +data.frame(matrix(unlist(strsplit(unlist(strsplit(qc$del[delSel], "\\|")), ":")), ncol=2, byrow=T)) -> dels +dels$ln <- nchar(as.vector(dels$X1)) +colnames(dels) <- c("seq", "occ", "ln") +delPees <- ppois(1:50, mean(rep(dels$ln, dels$occ)), lower.tail=F) +} + +insSel <- qc$ins != "." & !homFilt +if (sum(insSel) > 0) { +data.frame(matrix(unlist(strsplit(unlist(strsplit(qc$ins[insSel], "\\|")), ":")), ncol=2, byrow=T)) -> inss +inss$ln <- nchar(as.vector(inss$X1)) +colnames(inss) <- c("seq", "occ", "ln") +insPees <- ppois(1:50, mean(rep(inss$ln, inss$occ)), lower.tail=F) +} +# Calculate transition bias + + +#calcTransCor(qc) -> pCor +globalProb <- sum(qc$nVar) / (sum(qc$nRef) + sum(qc$nVar)) +# Calculate errorrate per amplicon +amps <- unique(qc$amp) +for (i in amps) { + print(i) + sel <- qc$amp == i + prob1 <- sum(qc$nVar[sel]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) + prob <- prob1 * calcTransCor(qc[sel,], lociFilt) + pees <- pbinom(qc$nVar[sel], qc$nRef[sel] + qc$nVar[sel], prob , lower.tail=F) + qc$pVal[sel] <- pees +# pois <- ppois(qc$nVar[sel], (qc$nRef + qc$nVar) * prob, lower.tail=F) +# qc$pValPois[sel] <- pois + + # Seperate for indel/deletion events + selDels <- delSel & sel + if (sum(selDels) > 0) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[selDels]), "\\|")), ":")), ncol=2, byrow=T)) -> dels2 + dels2$ln <- nchar(as.vector(dels2$X1)) + colnames(dels2) <- c("seq", "occ", "ln") + dels2$occ <- as.numeric(as.vector(dels2$occ)) + + for (j in which(selDels)) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[j]), "\\|")), ":")), ncol=2, byrow=T)) -> dels + dels$ln <- nchar(as.vector(dels$X1)) + colnames(dels) <- c("seq", "occ", "ln") + dels$occ <- as.numeric(as.vector(dels$occ)) + #dels$pDel <- delPees[as.integer(dels$ln)] + #dels$pVal <- ppois(as.numeric(dels$occ), dels$pDel, lower.tail=F) + dels$pDel <- sapply(dels$ln, function(x) {sum(dels2$occ[dels2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) + dels$pVal <- pbinom(dels$occ, qc$dp[j], dels$pDel, lower.tail=F) + dels$Q <- -10 * log10(dels$pVal) + + high <- order(dels$occ, -dels$Q, decreasing=T)[1] + qc$del[j] <- paste(dels$seq[high], dels$occ[high], sep=":") + qc$qScoreD[j] <- dels$Q[high] + pVal.D[j] <- dels$pVal[high] + } + } + selIns <- insSel & sel + if (sum(selIns) > 0) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[selIns]), "\\|")), ":")), ncol=2, byrow=T)) -> inss2 + inss2$ln <- nchar(as.vector(inss2$X1)) + colnames(inss2) <- c("seq", "occ", "ln") + inss2$occ <- as.numeric(as.vector(inss2$occ)) + + for (j in which(selIns)) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[j]), "\\|")), ":")), ncol=2, byrow=T)) -> inss + inss$ln <- nchar(as.vector(inss$X1)) + colnames(inss) <- c("seq", "occ", "ln") + inss$occ <- as.numeric(as.vector(inss$occ)) + #inss$pIns <- insPees[as.integer(inss$ln)] + #inss$pVal <- ppois(as.numeric(inss$occ), inss$pIns, lower.tail=F) + inss$pIns <- sapply(inss$ln, function(x) {sum(inss2$occ[inss2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) + inss$pVal <- pbinom(inss$occ, qc$dp[j], inss$pIns, lower.tail=F) + inss$Q <- -10 * log10(inss$pVal) + + high <- order(inss$occ, -inss$Q, decreasing=T)[1] + qc$ins[j] <- paste(inss$seq[high], inss$occ[high], sep=":") + qc$qScoreI[j] <- inss$Q[high] + pVal.I[j] <- inss$pVal[high] +} } + print(sum(-10 * log10(pees) > 100)) + print(sum(qc$qScoreI[selIns] > 100)) + print(sum(qc$qScoreD[selDels] > 100)) +} + +p.adjust(qc$pVal) -> qc$pValAdj +-10 * log(p.adjust(pVal.I)) -> qc$qScoreI +-10 * log(p.adjust(pVal.D)) -> qc$qScoreD +qc$qScore <- -10 * log10(qc$pValAdj) +#qc$qScore[qc$pValAdj == 0] <- 1000 +qc$qScore[qc$qScore > 1000] <- 1000 +qc$qScoreI[qc$qScoreI > 1000] <- 1000 +qc$qScoreD[qc$qScoreD > 1000] <- 1000 +qsel <- (qc$qScore >= 100 & qc$nVar >= 10) | (qc$qScoreI >= 200) | (qc$qScoreD >= 200) +dpfilt <- as.numeric(qc$dp) >= 100 +#varfilt <- as.numeric(qc$nVar) >= 10 + +selection <- qsel & dpfilt + +print(paste("Filtered out: ", sum(!selection), sep="")) +print(paste("Variants selected: ", sum(selection), sep="")) +return(qc) +} + + +addQualVarCor <- function(qc) { +# Corrected for variant occurence + +qc$del <- as.character(as.vector(qc$del)) +qc$ins <- as.vector(qc$ins) +qc$pVal <- 1 +qc$pValAdj <- 1 +#qc$pValPois <- 1 +qc$qScore <- 0 +qc$qScoreI <- 0 +qc$qScoreD <- 0 + +pVal.I <- rep(1, nrow(qc)) +pVal.D <- rep(1, nrow(qc)) + +delSel <- qc$del != "." +data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[delSel]), "\\|")), ":")), ncol=2, byrow=T)) -> dels +dels$ln <- nchar(as.vector(dels$X1)) +colnames(dels) <- c("seq", "occ", "ln") +delPees <- ppois(1:50, mean(rep(dels$ln, dels$occ)), lower.tail=F) + +insSel <- qc$ins != "." +data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[insSel]), "\\|")), ":")), ncol=2, byrow=T)) -> inss +inss$ln <- nchar(as.vector(inss$X1)) +colnames(inss) <- c("seq", "occ", "ln") +insPees <- ppois(1:50, mean(rep(dels$ln, dels$occ)), lower.tail=F) + +# Calculate base bias per run +sum(qc$nA[grepl("A", qc$ntRef, ignore.case=T)]) -> refA +sum(qc$nA[!grepl("A", qc$ntRef, ignore.case=T)]) -> varA +sum(qc$nC[grepl("C", qc$ntRef, ignore.case=T)]) -> refC +sum(qc$nC[!grepl("C", qc$ntRef, ignore.case=T)]) ->varC +sum(qc$nG[grepl("G", qc$ntRef, ignore.case=T)]) -> refG +sum(qc$nG[!grepl("G", qc$ntRef, ignore.case=T)]) -> varG +sum(qc$nT[grepl("T", qc$ntRef, ignore.case=T)]) -> refT +sum(qc$nT[!grepl("T", qc$ntRef, ignore.case=T)]) -> varT + +varA / (refA + varA) -> errA +varC / (refC + varC) -> errC +varG / (refG + varG) -> errG +varT / (refT + varT) -> errT +c(errA, errC, errG, errT) / mean(c(errA, errC, errG, errT)) -> errACGT + +errMat <- qc[,9:12] +errMat[grepl("A", qc$ntRef, ignore.case=T),1] <- 0 +errMat[grepl("C", qc$ntRef, ignore.case=T),2] <- 0 +errMat[grepl("G", qc$ntRef, ignore.case=T),3] <- 0 +errMat[grepl("T", qc$ntRef, ignore.case=T),4] <- 0 + +pCor <- rep(1, nrow(qc)) +pCor[grepl("^A", qc$ntVar, ignore.case=T)] <- errACGT[1] +pCor[grepl("^C", qc$ntVar, ignore.case=T)] <- errACGT[2] +pCor[grepl("^G", qc$ntVar, ignore.case=T)] <- errACGT[3] +pCor[grepl("^T", qc$ntVar, ignore.case=T)] <- errACGT[4] + +# Calculate errorrate per amplicon +amps <- unique(qc$amp) +for (i in amps) { + print(i) + sel <- qc$amp == i + prob <- sum(qc$nVar[sel]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) + #prob <- median(qc$nVar[sel] / (qc$nRef[sel] + qc$nVar[sel])) + pees <- pbinom(qc$nVar[sel], qc$nRef[sel] + qc$nVar[sel], prob * pCor[sel], lower.tail=F) + qc$pVal[sel] <- pees +# pois <- ppois(qc$nVar[sel], (qc$nRef + qc$nVar) * prob, lower.tail=F) +# qc$pValPois[sel] <- pois + + # Seperate for indel/deletion events + selDels <- delSel & sel + if (sum(selDels) > 0) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[selDels]), "\\|")), ":")), ncol=2, byrow=T)) -> dels2 + dels2$ln <- nchar(as.vector(dels2$X1)) + colnames(dels2) <- c("seq", "occ", "ln") + dels2$occ <- as.numeric(as.vector(dels2$occ)) + } + for (j in which(selDels)) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[j]), "\\|")), ":")), ncol=2, byrow=T)) -> dels + dels$ln <- nchar(as.vector(dels$X1)) + colnames(dels) <- c("seq", "occ", "ln") + dels$occ <- as.numeric(as.vector(dels$occ)) + #dels$pDel <- delPees[as.integer(dels$ln)] + #dels$pVal <- ppois(as.numeric(dels$occ), dels$pDel, lower.tail=F) + dels$pDel <- sapply(dels$ln, function(x) {sum(dels2$occ[dels2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) + dels$pVal <- pbinom(dels$occ, qc$dp[j], dels$pDel, lower.tail=F) + dels$Q <- -10 * log10(dels$pVal) + + high <- order(dels$occ, -dels$Q, decreasing=T)[1] + qc$del[j] <- paste(dels$seq[high], dels$occ[high], sep=":") + qc$qScoreD[j] <- dels$Q[high] + pVal.D[j] <- dels$pVal[high] + } + selIns <- insSel & sel + if (sum(selIns) > 0) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[selIns]), "\\|")), ":")), ncol=2, byrow=T)) -> inss2 + inss2$ln <- nchar(as.vector(inss2$X1)) + colnames(inss2) <- c("seq", "occ", "ln") + inss2$occ <- as.numeric(as.vector(inss2$occ)) + } + for (j in which(selIns)) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[j]), "\\|")), ":")), ncol=2, byrow=T)) -> inss + inss$ln <- nchar(as.vector(inss$X1)) + colnames(inss) <- c("seq", "occ", "ln") + inss$occ <- as.numeric(as.vector(inss$occ)) + #inss$pIns <- insPees[as.integer(inss$ln)] + #inss$pVal <- ppois(as.numeric(inss$occ), inss$pIns, lower.tail=F) + inss$pIns <- sapply(inss$ln, function(x) {sum(inss2$occ[inss2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) + inss$pVal <- pbinom(inss$occ, qc$dp[j], inss$pIns, lower.tail=F) + inss$Q <- -10 * log10(inss$pVal) + + high <- order(inss$occ, -inss$Q, decreasing=T)[1] + qc$ins[j] <- paste(inss$seq[high], inss$occ[high], sep=":") + qc$qScoreI[j] <- inss$Q[high] + pVal.I[j] <- inss$pVal[high] + } + print(sum(-10 * log10(pees) > 100)) + print(sum(qc$qScoreI[selIns] > 100)) + print(sum(qc$qScoreD[selDels] > 100)) +} + +p.adjust(qc$pVal) -> qc$pValAdj +-10 * log(p.adjust(pVal.I)) -> qc$qScoreI +-10 * log(p.adjust(pVal.D)) -> qc$qScoreD +qc$qScore <- -10 * log10(qc$pValAdj) +#qc$qScore[qc$pValAdj == 0] <- 1000 +qc$qScore[qc$qScore > 1000] <- 1000 +qc$qScoreI[qc$qScoreI > 1000] <- 1000 +qc$qScoreD[qc$qScoreD > 1000] <- 1000 +qsel <- (qc$qScore >= 100 & qc$nVar >= 10) | (qc$qScoreI >= 200) | (qc$qScoreD >= 200) +dpfilt <- as.numeric(qc$dp) >= 100 +#varfilt <- as.numeric(qc$nVar) >= 10 + +selection <- qsel & dpfilt + +print(paste("Filtered out: ", sum(!selection), sep="")) +print(paste("Variants selected: ", sum(selection), sep="")) +return(qc) +} + +#addQual(qc) -> qc +#write.table(qc, output, row.names=F, col.names=T, quote=F, sep="\t") +#write.table(qc[selection,], output, row.names=F, col.names=T, quote=F, sep="\t") + +calcTrans <- function(qcRaw, lociFilt = NULL) { + +sel <- rep(T, nrow(qcRaw)) +if (!is.null(lociFilt)) { +paste(qcRaw$X.chr, qcRaw$pos, sep=":") -> qcpos +sel <- ! qcpos %in% lociFilt +} +qc <- qcRaw[sel,] + +print(sum(sel)) + +# Calculate transition bias +refA <- grepl("A", qc$ntRef, ignore.case=T) +refC <- grepl("C", qc$ntRef, ignore.case=T) +refG <- grepl("G", qc$ntRef, ignore.case=T) +refT <- grepl("T", qc$ntRef, ignore.case=T) +varA <- grepl("A", qc$ntVar, ignore.case=T) +varC <- grepl("C", qc$ntVar, ignore.case=T) +varG <- grepl("G", qc$ntVar, ignore.case=T) +varT <- grepl("T", qc$ntVar, ignore.case=T) +varN <- grepl(".", qc$ntVar, ignore.case=T) +callA <- grepl("^A", qc$ntVar, ignore.case=T) +callC <- grepl("^C", qc$ntVar, ignore.case=T) +callG <- grepl("^G", qc$ntVar, ignore.case=T) +callT <- grepl("^T", qc$ntVar, ignore.case=T) + +callList <- list(callA, callC, callG, callT) +varList <- list(varA, varC, varG, varT) +refList <- list(refA, refC, refG, refT) + +#tots <- c( +#rep(sum(qc$nRef[refA], qc$nVar[refA]), 4), +#rep(sum(qc$nRef[refC], qc$nVar[refC]), 4), +#rep(sum(qc$nRef[refG], qc$nVar[refG]), 4), +#rep(sum(qc$nRef[refT], qc$nVar[refT]), 4)) + +nvar <- c( +rep(sum(qc$nC[refA], qc$nG[refA], qc$nT[refA]), 4), +rep(sum(qc$nA[refC], qc$nG[refC], qc$nT[refC]), 4), +rep(sum(qc$nA[refG], qc$nC[refG], qc$nT[refG]), 4), +rep(sum(qc$nA[refT], qc$nC[refT], qc$nG[refT]), 4)) + +ncall <- c( +rep(sum(qc$nVar[refA]), 4), +rep(sum(qc$nVar[refC]), 4), +rep(sum(qc$nVar[refG]), 4), +rep(sum(qc$nVar[refT]), 4)) + +nref <- c( +rep(sum(qc$nRef[refA]), 4), +rep(sum(qc$nRef[refC]), 4), +rep(sum(qc$nRef[refG]), 4), +rep(sum(qc$nRef[refT]), 4)) + +tots <- nref + nvar + +nts <- c("A", "C", "G", "T") +sumTrans <- data.frame(trans=paste(rep(nts, each=4), rep(nts, 4), sep=":"), cnt=rep(0, 16), tot=tots, nvar=nvar, nref=nref, ncall=ncall) + +for (i in 1:4) { + pos <- (i - 1) * 4 +for (j in 1:4) { +# print(sum(refList[[i]] & varList[[j]])) + + cnt <- sum(qc[refList[[i]] & varList[[j]], 8 + j]) + if (i == j) { +# cnt <- sum(qc[refList[[i]] & varN, 8 + j]) + cnt <- NA + } + sumTrans$cnt[pos + j] <- cnt + print(cnt) +}} + +#sumTrans$cnt / sumTrans$nvar / sumTrans$tot * 1000000 -> tmp +sumTrans$cnt / sumTrans$tot * 1000000 -> tmp + +#totalNT <- sum(qc$nVar) + sum(qc$nRef) +#sumTrans$cnt / median(sumTrans$cnt, na.rm=T) -> sumTrans$cor +sumTrans$cnt / median(sumTrans$cnt, na.rm=T) -> sumTrans$cor +tmp / median(tmp, na.rm=T) -> sumTrans$cor2 +#sumTrans$cnt / totalNT -> sumTrans$cor +#sumTrans$cnt / min(sumTrans$cnt, na.rm=T) -> sumTrans$cor + + +return(sumTrans) + +} + +calcTransCor <- function(qcRaw, lociFilt = NULL) { + +calcTrans(qcRaw, lociFilt) -> sumTrans + +pCor <- rep(1, nrow(qcRaw)) +paste(qcRaw$ntRef, substr(qcRaw$ntVar, 1, 1), sep=":") -> qcTrans + +for (i in c("A", "C", "G", "T")) { +for (j in c("A", "C", "G", "T")) { + if (i != j) { + tTrans <- paste(i, j, sep=":") + pCor[grepl(tTrans, qcTrans, ignore.case=T)] <- sumTrans$cor2[sumTrans$trans == tTrans] + } + +}} +return(pCor) +} + + +calcTransCorOld <- function(qc) { +# Calculate transition bias +refA <- grepl("A", qc$ntRef, ignore.case=T) +refC <- grepl("C", qc$ntRef, ignore.case=T) +refG <- grepl("G", qc$ntRef, ignore.case=T) +refT <- grepl("T", qc$ntRef, ignore.case=T) +varA <- grepl("A", qc$ntVar, ignore.case=T) +varC <- grepl("C", qc$ntVar, ignore.case=T) +varG <- grepl("G", qc$ntVar, ignore.case=T) +varT <- grepl("T", qc$ntVar, ignore.case=T) +varN <- grepl(".", qc$ntVar, ignore.case=T) +callA <- grepl("^A", qc$ntVar, ignore.case=T) +callC <- grepl("^C", qc$ntVar, ignore.case=T) +callG <- grepl("^G", qc$ntVar, ignore.case=T) +callT <- grepl("^T", qc$ntVar, ignore.case=T) + +callList <- list(callA, callC, callG, callT) +varList <- list(varA, varC, varG, varT) +refList <- list(refA, refC, refG, refT) + +tots <- c( +rep(sum(qc$nRef[refA], qc$nVar[refA]), 4), +rep(sum(qc$nRef[refC], qc$nVar[refC]), 4), +rep(sum(qc$nRef[refG], qc$nVar[refG]), 4), +rep(sum(qc$nRef[refT], qc$nVar[refT]), 4)) + +nvar <- c( +rep(sum(qc$nVar[refA]), 4), +rep(sum(qc$nVar[refC]), 4), +rep(sum(qc$nVar[refG]), 4), +rep(sum(qc$nVar[refT]), 4)) + +nref <- c( +rep(sum(qc$nRef[refA]), 4), +rep(sum(qc$nRef[refC]), 4), +rep(sum(qc$nRef[refG]), 4), +rep(sum(qc$nRef[refT]), 4)) + +nts <- c("A", "C", "G", "T") +sumTrans <- data.frame(trans=paste(rep(nts, each=4), rep(nts, 4), sep=":"), cnt=rep(0, 16), tot=tots, nvar=nvar, nref=nref) + +for (i in 1:4) { + pos <- (i - 1) * 4 +for (j in 1:4) { +# print(sum(refList[[i]] & varList[[j]])) + + cnt <- sum(qc[refList[[i]] & varList[[j]], 8 + j]) + if (i == j) { +# cnt <- sum(qc[refList[[i]] & varN, 8 + j]) + cnt <- NA + } + sumTrans$cnt[pos + j] <- cnt + print(cnt) +}} +#totalNT <- sum(qc$nVar) + sum(qc$nRef) +sumTrans$cnt / median(sumTrans$cnt, na.rm=T) -> sumTrans$cor +#sumTrans$cnt / totalNT -> sumTrans$cor +#sumTrans$cnt / min(sumTrans$cnt, na.rm=T) -> sumTrans$cor +print(sumTrans) + +pCor <- rep(1, nrow(qc)) +for (i in 1:4) { + pos <- (i - 1) * 4 +for (j in 1:4) { + if (i != j) { + pCor[refList[[i]] & callList[[j]]] <- sumTrans$cor[pos + j] + } + +}} +return(pCor) +} diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/getData.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/getData.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,140 @@ +#!/usr/bin/perl + +use strict; + +# Read in path(s) and run bcl2fastq to fetch data into appropriate directories + +my $runDir = shift; +my $project = shift || die "Project required"; +my $baseDir = shift || "/ccagc/data/SeqAnalysis/$project"; +my $dry = 0; +my $outDir = undef; +(my $FCID = $runDir) =~ s/.*_(.*?)\/?$/$1/; + +if (not defined($outDir)) { + ($outDir = $runDir) =~ s/.*\/(.*_.*_.*)_.*/$1/; + $outDir = $baseDir ."/". $outDir; +} + +print STDERR localtime() . " : PATH: " . $runDir . "\n"; +print STDERR localtime() . " : BASEDIR: " . $baseDir . "\n"; +print STDERR localtime() . " : OUTDIR: " . $outDir . "\n"; +print STDERR localtime() . " : FCID: " . $FCID . "\n"; + +# open samplesheet +# Check run type and convert for bcl2fastq +my $col = 0; + +my @headOut = qw/FCID Lane SampleID SampleRef Index Description Control Recipe Operator SampleProject/; +my $Lane = 1; +my $SampleRef = "human"; +my $Control = "N"; +my $SampleProject = $project; +my %header = (); +open SAMPLE, "<$runDir/SampleSheet.csv" or die; +while () { + chomp; + s/\s+$//; + my @row = split(/,/, $_); +# if (/^(.*),(.*)$/) { +# $header{$1} = $2; +# } + $header{$row[0]} = $row[1]; + last if (/\[Data\]/); +} + +if ($header{Assay} !~ /Amplicon/) { + print STDERR localtime() . " : Wrong assay, exiting.\n"; + exit; +} + +# Skipping project name check for now +#if ($header{"Project Name"} !~ /$project/) { +# print STDERR localtime() . " : Wrong project, exiting.\n"; +# exit; +#} + +my $Operator = $header{"Investigator Name"}; +my $Recipe = $header{"Workflow"}; + +my $head = readline(SAMPLE); +chomp $head; +my %headIn = map { $_ => $col++ } split(/,/, $head);#"Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description,Manifest,GenomeFolder"); + +my @samples = (); +my @ctrls = (); +while () { + chomp; + my @row = split(/,/, $_); + print STDERR localtime() . " : " . join(":", @row) . "\n"; + my $bc = substr($row[$headIn{index}],0,7) ."-". substr($row[$headIn{index2}],0,7); + if ($row[$headIn{Sample_Project}] != /$SampleProject/) { + push @samples, join(",", $FCID, $Lane, $row[$headIn{Sample_ID}], $SampleRef, $bc, $row[$headIn{Description}], $Control, $Recipe, $Operator, $SampleProject) . "\n"; + } + elsif ($row[$headIn{Sample_Project}] != /CONTROL/i) { + push @ctrls, join(",", $FCID, $Lane, $row[$headIn{Sample_ID}], $SampleRef, $bc, $row[$headIn{Description}], $Control, $Recipe, $Operator, $SampleProject) . "\n"; + } + +} +close SAMPLE; + +if ($dry == 1) { + print STDERR localtime() . " : mkdir $outDir\n"; + print STDERR localtime() . " : " . join(",", @headOut) . "\n"; + print STDERR localtime() . " : " . join("", @samples); +} +elsif (-e $outDir) { + print STDERR localtime() . " : Folder $outDir exists, exiting\n"; + exit; +} +elsif ($#samples >= 0) { + print STDERR localtime() . " : mkdir $outDir\n"; + system("mkdir -p $outDir"); + open SAMPLEOUT, ">$outDir/SampleSheet.csv"; + print SAMPLEOUT join(",", @headOut) . "\n"; + print STDERR localtime() . " : " . join(",", @headOut) . "\n"; + print SAMPLEOUT join("", @samples, @ctrls); + print STDERR localtime() . " : " . join("", @samples, @ctrls); + close SAMPLEOUT; +} +else { + # Nothing to do exit! + print STDERR localtime() . " : Nothing to do for $SampleProject, exiting!"; + exit; +} + + +# run configureBCL2fastq +my $bcl2fqbin = "/usr/local/bin/configureBclToFastq.pl"; +my $bcl2fq = "$bcl2fqbin --no-eamss --input-dir $runDir/Data/Intensities/BaseCalls --output-dir $outDir/Unaligned --sample-sheet $outDir/SampleSheet.csv --mismatches 0 --fastq-cluster-count 0"; +my $make = "cd $outDir/Unaligned && nohup make && touch bcl2fq.done && cd .."; + +print STDERR localtime() . " : $bcl2fq\n"; +print STDERR localtime() . " : $make\n"; +if ($dry == 1) { + exit; +} + +my $pid1 = open BCL2FQ, "$bcl2fq 2>&1 |"; +while () { + print STDERR localtime() . " - $_"; +} +close BCL2FQ; + +my $pid2 = open MAKE, "$make 2>&1 |"; +while () { + print STDERR localtime() . " - $_"; +} +close MAKE; + + +#my $rc1 = 0; #system($bcl2fq); +# run make +#if ($rc1 == 0) { +# my $rc2 = system($make); +#} +#else { +# print STDERR localtime() . " : Error or warning encountered :$rc1\n"; +# print STDERR localtime() . " : Run make manually\n"; +# print STDERR localtime() . " : $make\n"; +#} diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/mkHtmlReport.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/mkHtmlReport.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,201 @@ +#!/usr/bin/perl -w + +use strict; +use Spreadsheet::WriteExcel; + +$| = 1; +my $dir = shift; +my $outdir = shift || "./"; +my $pat = shift || ""; + +# QC +# Results +my @samples = (); +open INDEX, ">$outdir/index.html"; +my $htmlHead = qq( + + + + + + +); +print INDEX $htmlHead; +opendir DIR, "$dir"; +while (my $cd = readdir DIR) { + if ($cd =~ /(.*$pat)\.qc\.targets\.txt$/) { + my $sam = $1; +# next if ($sam =~ /R[12]/); + print STDERR $1 . "\n"; + push @samples, $1; + } +} +close DIR; + +print INDEX ""; +print INDEX "\n"; +#foreach my $sam (sort @samples) { +# print INDEX "\n"; + +#} +my %link = (); + +foreach my $sample (sort @samples) { + print STDERR "Processing $sample\n"; +# next if ($sample =~ /R[12]/); + + my $readCnt = 0; + my $amp100 = 0; + + open OUT, ">$outdir/$sample.html"; + open OUT2, ">$outdir/$sample.tsv"; + my $excelBook = Spreadsheet::WriteExcel->new("$outdir/$sample.xls"); + my $excel = $excelBook->add_worksheet(); + print OUT $htmlHead; + my %QC = (); + open QC, "<$dir/$sample.qc.targets.txt"; + readline QC; + print STDERR "Reading in $sample.qc.targets.txt\n"; + while () { + chomp; + my @row = split(/\t/, $_); + my @id = split(/[\_\.\-:]/, $row[0]); + $readCnt += $row[-1]; # DP + $amp100++ if ($row[-1] >= 100); # + if ($#id != 10) { + $id[0] =~ /(\D+)(\d+)/; + $id[0] = $2; + unshift @id, $1; + } + $QC{$row[0]}{QC} = [@id, @row];# if ($id[0]); + foreach my $c ($row[4] .. $row[5]) { + $link{$id[-3] . ":" . $c}{$row[0]} = "Assay"; + } + foreach my $c ($row[2] .. $row[4], $row[5] .. $row[3]) { + $link{$id[-3] . ":" . $c}{$row[0]} = "LSO"; + } + } + close QC; + + open RES, "<$dir/$sample.res.filtered.tsv" or die "Unable to open $dir/$sample\n"; + my %uniq = (); + my $colCnt = 0; + my $resHead = readline(RES); + chomp $resHead; + $resHead =~ s/^#//; + $resHead =~ s/\s+$//; + my %resCol = map { $_ => $colCnt++ } split(/\t/, $resHead); + my @keyColsN = qw/QUAL Gene_Name Codon_Change Amino_Acid_change vaf DP AD Tag CHROM POS ID REF ALT Context Effect_Impact Functional_Class Amino_Acid_length Gene_Coding Transcript_ID Exon_Rank/; + #my @keyColsN = qw/QUAL Gene_Name Codon_Change Amino_Acid_change vaf DP AD Tag CHROM POS ID REF ALT Context Effect_Impact Functional_Class Amino_Acid_length Coding Transcript Exon/; +# my @keyColsN = qw/CHROM POS ID REF ALT QUAL DP AD vaf Context Effect_Impact Functional_Class Codon_Change Amino_Acid_change Amino_Acid_length Gene_Name Coding Transcript Exon Tag/; + my @keyColsI = map { $resCol{$_} } @keyColsN; +# print STDERR join(":", @keyColsN) . "\n"; +# print STDERR join(":", @keyColsI) . "\n"; +# sleep 10; + print STDERR "Processing results\n"; + while () { + chomp; + my @row = split(/\t/, $_); + my $cpos = join(":", @row[0, 1]); + if (exists $link{$cpos}) { +# my $key = join(":", @row[0 .. 4,6, 9,10,11,12,14 .. 21]); + my $key = join(":", @row[@keyColsI]); + #print STDERR join(":", @keyColsI) . "\n"; +# print STDERR join(":", @row) . "\n"; sleep 1; + if (not exists($uniq{$key})) { + foreach my $locus (keys(%{$link{$cpos}})) { + next if ($link{$cpos}{$locus} eq "LSO"); + push @{$QC{$locus}{RES}}, [@row, $link{$cpos}{$locus}]; + # print STDERR "Adding $key to $locus\n\n"; #sleep 1; + } + $uniq{$key} = 0; + } + else { + # print STDERR $key . " : Exists\n\n"; #sleep 1; + } + } + } + close RES; + print OUT "

"; + print OUT "

"; + #print OUT "

"; + print OUT "

Sample	BAM	snp	indel	readCnt	Amp > 100
$sam	BAM	BAI

"; + print OUT "

Download:	TSV	XLS

"; + print OUT "\n"; +# my @colnames = qw/depth chr pos id ref var qual DP AD vaf context impact effectClass codonChange AAChange RefSeqLength geneName RefSeqClass RefSeqID Exon Tag/; + my @colnames = ("depth", @keyColsN); + print OUT "" . join("", map { "" } ("Amplicon", "c","c2", "b", @colnames)) . ""; + print OUT2 join("\t", "Amplicon", @colnames) . "\n"; + my $excelAref = [["Amplicon", @colnames]]; + my %rescnt = (); + foreach my $locus (sort keys(%QC)) { + # my @targets = keys(%{$QC{$locus}{QC}}); +# print OUT ""; + my $nres = 1; + $nres = scalar(@{$QC{$locus}{RES}}) if ($QC{$locus}{RES}); + + print OUT "\n"; + print OUT "\n"; + print OUT "\n"; + print OUT "\n"; + print OUT "\n"; #\n"; + print OUT2 join("\t", $locus, $QC{$locus}{QC}->[-1], @{$res}[@keyColsI]) . "\n"; + push @$excelAref, [$locus, $QC{$locus}{QC}->[-1], @{$res}[@keyColsI]]; + my $pl = $res->[$keyColsI[7]]; + my $ref = $res->[$keyColsI[11]]; + my $var = $res->[$keyColsI[12]]; +# print STDERR "$pl $ref $var\n"; sleep 1; + if (length($ref) == length($var)) { + $rescnt{$pl . "snp"}++; + } + else { + $rescnt{$pl . "indel"}++; + } +# $rescnt++; + } + print STDERR $locus . ":" . $nres . "\n"; + print STDERR $locus . ":" . join("-", @{$QC{$locus}{RES}}) . "\n"; + if (scalar(@{$QC{$locus}{RES}}) == 0) { #$nres == 0) { + print OUT2 join("\t", $locus, $QC{$locus}{QC}->[-1], ("-") x scalar(@keyColsI)) . "\n"; + push @$excelAref, [$locus, $QC{$locus}{QC}->[-1], ("-") x scalar(@keyColsI)]; + } + print OUT "\n"; + } + print OUT "

$_
$locus	c	c2	b	$QC{$locus}{QC}->[-1]	"; + + foreach my $res (@{$QC{$locus}{RES}}) { + print OUT "	\n"; + print OUT join("	\n", @{$res}[@keyColsI]); + print OUT "

\n"; + print OUT "\n"; + close OUT; + close OUT2; + $excel->write_col(0,0, $excelAref); + $excelBook->close(); + my @resCnt = map { $rescnt{$_} || 0 } qw/Customsnp Customindel/; + my $pctGood = sprintf("%.2f", $amp100 / scalar(keys(%QC)) * 100); + print INDEX "$sample BAM$resCnt[0]$resCnt[1]$readCnt$pctGood\n"; + +} + +print INDEX ""; +print INDEX "

"; +print INDEX "

"; +print INDEX ""; +close INDEX; + + diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/pairUp.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/pairUp.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,56 @@ +#!/usr/bin/perl -w + +use strict; + +my $r1 = shift; +my $r2 = shift; +my $o1 = shift || "$r1.paired"; +my $o2 = shift || "$r2.paired"; +my $min = 10; +my %hsh = (); + +open R1, "<$r1"; +while () { + /(.*?)\s/; + my $k = $1; + my $h = $_; + my $seq = readline(R1); + my $qual = readline(R1); + $qual .= readline(R1); + if (length($seq) > $min) { + $hsh{$k} = $h . $seq . $qual; + } + else { +# print STDERR "$h$seq too short\n"; sleep 1; + } +} +close R1; + +open R2, "<$r2"; +open O1, ">$o1"; +open O2, ">$o2"; + +while () { + /(.*?)\s/; + my $k = $1; + my $h = $_; + my $seq = readline(R2); + my $qual = readline(R2); + $qual .= readline(R2); + if (length($seq) > $min) { + } + else { +# print STDERR "$h$seq too short\n"; sleep 1; + next; + } + if (exists($hsh{$k})) { + print O1 $hsh{$k}; + print O2 $h . $seq . $qual; + } + else { +# print STDERR "$k is missing\n"; sleep 1; + } +} +close R2; +close O1; +close O2; diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/perAmpliconAnalysis.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/perAmpliconAnalysis.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,354 @@ +#!/usr/bin/perl -w + +use strict; + +my $bam = shift; +my $ref = shift || "/gsdata/tmp/TSACP/ampliconPipeLine/ref/hg19/bwa-5/hg19.fa"; +my $manifest = shift || "/gsdata/tmp/TSACP/ampliconPipeLine/ref/manifests/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt"; +my $base = shift || "output"; +my $samtools = shift || "/gsdata/tmp/TSACP/ampliconPipeLine/bin/samtools/samtools-0.1.18/samtools"; +my $fai = $ref . ".fai"; + +open FAI, "<$fai"; +my %idx = (); +print STDERR "Reading fa index ... "; +while () { + chomp; + my @row = split(/\t/, $_); + $idx{$row[0]} = [@row]; +} +print STDERR "done\n"; + +close FAI; +open REF, "<$ref"; + +my %stats = (); +my %manif = (); +my %targets = (); +my %probe = (); +my %hash = (); + +open M, "<$manifest" or die "Unable to open manifest: $manifest\n" ; +while () { last if (/\[Probes\]/) } +readline(M); +while () { + chomp; + if (/\[Targets\]/) { + my $h = readline M; + chomp $h; + my @H = split(/\t/, $h); + last; + } + my @row = split(/\t/, $_); + $probe{$row[2]}{probe} = [@row]; + $probe{$row[2]}{ULSO} = $row[9]; + $probe{$row[2]}{DLSO} = $row[11]; +} + +while () { + chomp; + s/\s+$//; + my @row = split(/\t/, $_); + push @{$targets{$row[3]}{$_}}, $row[0] foreach ($row[4] .. $row[5]); + # $manif{$aTarget} = [@row]; + my $aTarget = $row[0] . "-" . $row[3] . ":". "$row[4]-$row[5]"; + if (not exists($stats{$aTarget}{target})) { + $stats{$aTarget}{target} = [@row]; + $stats{$aTarget}{ln} = $row[5] - $row[4] + 1; + $stats{$aTarget}{n} = 0; + $stats{$aTarget}{sam} = []; + $stats{$aTarget}{depth} = 0; + $stats{$aTarget}{covs} = []; + $stats{$aTarget}{chr} = $row[3]; + $stats{$aTarget}{start} = $row[4]; + $stats{$aTarget}{end} = $row[5]; + $stats{$aTarget}{ULSO} = $probe{$row[0]}{ULSO}; + $stats{$aTarget}{DLSO} = $probe{$row[0]}{DLSO}; + $stats{$aTarget}{assayStart} = $row[4] + length($probe{$row[0]}{ULSO}); + $stats{$aTarget}{assayEnd} = $row[5] - length($probe{$row[0]}{DLSO}); + } +# print $row[0] . "\n"; + foreach my $i (0 .. 5) { + foreach my $j (0 .. 5) { +# print $row[4] + $i .":". ($row[5] - $row[4] + $j) .":". $row[0] . "\n"; +# print $row[4] + $i .":". ($row[5] - $row[4] - $j) .":". $row[0] . "\n"; +# print $row[4] - $i .":". ($row[5] - $row[4] + $j) .":". $row[0] . "\n"; +# print $row[4] - $i .":". ($row[5] - $row[4] - $j) .":". $row[0] . "\n"; + $hash{$row[3]}{$row[4] + $i}{$row[5] - $row[4] + $j} = $aTarget; + $hash{$row[3]}{$row[4] + $i}{$row[5] - $row[4] - $j} = $aTarget; + $hash{$row[3]}{$row[4] - $i}{$row[5] - $row[4] + $j} = $aTarget; + $hash{$row[3]}{$row[4] - $i}{$row[5] - $row[4] - $j} = $aTarget; + } + } +# sleep 1; +} +close M; + +# samtools view -b 25MUT5.bam chr9:133738302-133738491 | samtools calmd - /gsdata/tmp/TSACP/ampliconPipeLine/ref/hg19/bwa-5/hg19.fa | head + +#foreach my $amp (keys(%stats)) { + +# print $amp . "\n"; +# my @SAM = (); + # Fetch reads +# my $coord = $stats{$amp}{chr} .":".$stats{$amp}{start}."-".$stats{$amp}{end}; +# my $ln = $stats{$amp}{ln}; +# print $coord . " $ln\n"; + +# Open output +open QC, ">$base.qc.ann.txt"; +open QC2, ">$base.qc2.ann.txt"; +open TARGET, ">$base.qc.targets.txt"; + +#TODO Remove stampy check +my $stampy = 0; +open SAMH, "$samtools view -H $bam |"; +while () { + $stampy = 1 if (/PN:stampy/); + print STDERR "STAMPY SPOTTED!!!" if (/PN:stampy/); +} +close SAMH; + +open SAM, "$samtools view $bam |"; +#open SAM, "$samtools view -b $bam | $samtools calmd - $ref |"; +# open SAM, "$samtools view -b $bam $coord | $samtools calmd - $ref |"; +while () { + last unless (/^@/); +} +my $cnt = 0; +my %hsh = (); +my $pamp = "."; + +#Print header + +print QC "#" . join("\t", qw/chr pos amp dp ntRef ntVar nRef nVar nA nC nG nT nN ins del/) . "\n"; +print QC2 "#" . join("\t", qw/read chr pos amp event/) . "\n"; +print TARGET "#" . join("\t", qw/amp chr start end assayStart assayEnd depth/) . "\n"; +while () { + # Skip stampy reads? Nope, stampy is no longer needed + #TODO Remove stampy check +# next if ($stampy == 1 && ! /XP:Z:BWA/); + chomp; + my @row = split(/\t/, $_); + my $l = 0; + my $cig = $row[5]; + $cig =~ s/(\d+)[MD]/$l+=$1/eg; + + my $amp = $hash{$row[2]}{$row[3]}{$l} || next; + #print "$row[2] $row[3] $l $amp\n"; + + push @{$stats{$amp}{sam}}, [@row]; + $stats{$amp}{depth}++; + if (($pamp ne ".") && ($amp ne $pamp)) { + print STDERR "Flushing $pamp $stats{$pamp}{depth}\n"; +# print TARGET join("\t", $pamp, map { $stats{$pamp}{$_} } qw/chr start end assayStart assayEnd depth/) . "\n"; + my $data = &call($stats{$pamp}{sam}); + &flush($data, $stats{$pamp}{chr}, $pamp, $stats{$pamp}{assayStart}, $stats{$pamp}{assayEnd}); + $stats{$pamp}{sam} = []; + } + $pamp = $amp; + $cnt++; +} + +close QC; +close QC2; +foreach my $pamp (keys %stats) { + print TARGET join("\t", $pamp, map { $stats{$pamp}{$_} || "NA"} qw/chr start end assayStart assayEnd depth/) . "\n"; +} +close TARGET; + + +# print join("\n", map {$hsh{$_} . ":" . $_} keys(%hsh)) . "\n"; +# print $cnt . "\n"; sleep 1; + close SAM; +# $stats{$amp}{depth} = $cnt; +# my $data = &call(\@SAM); +# &flush($data, $stats{$amp}{chr}, $amp); + +#} + +#foreach my $amp (keys(%stats)) { + +# print $amp . ":" . scalar(@{$stats{$amp}{sam}}) . "\n"; +#} + +sub call { + my $SAM = shift; + + my $ppos = 0; + my $pchr = ""; + my %data = (); + my $refSeq = ""; + my $c = 0; + my $col_chr = 2; + my $col_read = 9; + my $col_qual = 10; + my $col_pos = 3; + my $col_cigar = 5; + my $refSeqPad = "P"; + my %cooc = (); + my $cnt = 1; + foreach my $r (0 .. $#$SAM) { + my @row = @{$SAM->[$r]}; + my $read = $row[$col_read]; + my $qual = $row[$col_qual]; + my $pos = $row[$col_pos]; + my @cig = (); + my $aln = 0; + while ($row[$col_cigar] =~ /(\d+)(\D)/g) { + push @cig, [$1, $2]; + $aln += $1; + } + if ($ppos != $pos) { + my $offset = $idx{$row[$col_chr]}->[2]; + my $nl = int (($row[$col_pos] - 1) / $idx{$row[$col_chr]}->[3]); + $offset += $row[$col_pos] + $nl - 1; + seek REF, $offset, 0; + $refSeqPad = substr($refSeq, -1, 1); + read REF, $refSeq, 1000;# length($read) * 5; + $refSeq =~ s/\s//g; + $data{$row[$col_chr]}{$row[$col_pos] + $_}{"refNT"} = substr($refSeq, $_, 1) foreach (0 .. $aln); + $ppos = $pos; + } + + foreach my $cigE (@cig) { + my $n = $cigE->[0]; + if ($cigE->[1] eq "I") { + my $rpos = $pos - $row[$col_pos]; + my $insert = substr($refSeq, $rpos - 1, 1) or print STDERR "Outside?" . $rpos . ":" . length($refSeq) . " $pos\n"; + $insert .= substr($read, 0, $n, ""); + my $qinsert .= substr($qual, 0, $n, ""); + push @{$data{$row[$col_chr]}{$pos - 1}{"IR"}{$insert}}, $r; + $data{$row[$col_chr]}{$pos - 1}{"I"}{$insert}++; +# push @{$cooc{$pos - 1 }{$insert}}, $cnt; + # $cooc{($pos - 1) .":".$insert}{$cnt} = 0; + } + elsif ($cigE->[1] eq "M") { + my $mseq = substr($read, 0, $n, ""); + my $mqual = substr($qual, 0, $n, ""); + foreach my $nt (0 .. (length($mseq) - 1)) { + $data{$row[$col_chr]}{$pos + $nt}{"DP"}++; + my $ntq = substr($mqual, $nt, 1); + my $ntn = substr($mseq, $nt, 1); + if (ord($ntq) - 33 < 30) { + $ntn = "N"; + } + $data{$row[$col_chr]}{$pos + $nt}{"NT"}{$ntn}++; + push @{$data{$row[$col_chr]}{$pos + $nt}{"NTR"}{$ntn}}, $r if (uc($ntn) ne uc($data{$row[$col_chr]}{$pos + $nt}{refNT})); +# if (($ntn ne $data{$row[$col_chr]}{$pos + $nt}{"refNT"}) && ($ntn ne "N")) { + #push @{$cooc{$pos + $nt}{$ntn}}, $cnt; + # $cooc{($pos + $nt) .":".$ntn}{$cnt} = 0; +# } + } + $pos += $n; + + } + elsif ($cigE->[1] eq "D") { + my $rpos = $pos - $row[$col_pos]; + my $deletion = substr($refSeq, $rpos - 1, $n + 1); # Substring out of string error ? + push @{$data{$row[$col_chr]}{$pos - 1}{"DR"}{$deletion}}, $r; + $data{$row[$col_chr]}{$pos - 1}{"D"}{$deletion}++; + #push @{$cooc{$pos - 1 }{$deletion}}, $cnt; + # $cooc{($pos - 1) . ":" . $deletion}{$cnt} = 0; + $pos += $n; + } + } + $cnt++; + } + #my $thresh = scalar(@$SAM) * .05; + #&coocCalc(\%cooc, \%data, $thresh); + return \%data; +} + +sub coocCalc { + my $cooc = shift; + my $data = shift; + my $thresh = shift; + my %rev = (); + # Filter low frequency variants + foreach my $k (keys(%$cooc)) { + if (scalar(keys(%{$cooc->{$k}})) < $thresh) { + delete($cooc->{$k}); + next; + } + print STDERR "$k : $thresh : " . join(":", sort {$a cmp $b} keys(%{$cooc->{$k}})) . "\n"; + } + my @muts = keys(%{$cooc}); + foreach my $i (0 .. $#muts) { +# my %hsh = map { $_ => 0 } keys(%{$cooc{$muts[$i]}}); + foreach my $j (($i + 1) .. $#muts) { + my $score = 0; + foreach my $m (keys(%{$cooc->{$muts[$i]}})) { + if (exists($cooc->{$muts[$j]}{$m})) { + $score++; + } + } + print STDERR $muts[$i] .":". $muts[$j] . ":" . $score . "\n"; sleep 1; + } + } + + #{read}{mutation} + #{mutation}{read} + sleep 1; +} + +sub flush { + my $data = shift; + my $chr = shift; + my $amp = shift; + my $s = shift; + my $e = shift; + return unless (exists($data->{$chr})); + print STDERR "printing ... "; + my %reads = (); # read->pos->nt +# foreach my $p (sort {$a <=> $b} keys(%{$data->{$chr}})) { +# unless (($p >= $s) && ($p <= $e)) { +# next; +# } + foreach my $p ($s .. $e) { + my $posdat = $data->{$chr}{$p} || next; + next unless (exists($posdat->{DP})); + my $refNT = uc($posdat->{refNT}); + my @varOrd = sort { $posdat->{NT}{$b} <=> $posdat->{NT}{$a} } grep {$_ ne "N"} grep { $_ ne $refNT } keys(%{$posdat->{NT}}); + my $seqNT = join("/", @varOrd); + #my $refCNT = scalar(@{$posdat->{NT}{$refNT} || []}); + my $refCNT = $posdat->{NT}{$refNT} || 0; + my $varCNT = 0; + #$varCNT += scalar(@{$posdat->{NT}{$_}}) foreach (@varOrd); + #$varCNT += $posdat->{NT}{$_} foreach (@varOrd); + $varCNT = ($varOrd[0])?$posdat->{NT}{$varOrd[0]}:0; + my $Istr = "."; + my $Dstr = "."; + if ($varOrd[0]) { + $reads{$_}{$p} = "$refNT/$varOrd[0]" foreach (@{$posdat->{NTR}{$varOrd[0]}}); + } + if (exists($posdat->{I})) { + $Istr = join("|", map { $_ . ":" . $posdat->{I}{$_} } keys(%{$posdat->{I}})); + foreach my $I (keys(%{$posdat->{IR}})) { + $reads{$_}{$p} = "$refNT/$I" foreach (@{$posdat->{IR}{$I}}); + } + } + if (exists($posdat->{D})) { + $Dstr = join("|", map { $_ . ":" . $posdat->{D}{$_} } keys(%{$posdat->{D}})); + foreach my $D (keys(%{$posdat->{DR}})) { + $reads{$_}{$p} = "$D/$refNT" foreach (@{$posdat->{DR}{$D}}); + } + } + #$Dstr = join("|", map { $_ . ":" . $posdat->{D}{$_} } keys(%{$posdat->{D}})) if exists($posdat->{D}); + print QC join("\t", $chr, $p, $amp, + $posdat->{DP} || 0, + $posdat->{refNT} || ".", + $seqNT || ".", + $refCNT, $varCNT, + #(map { scalar(@{$posdat->{NT}{$_} || []})} qw(A C G T N)), $Istr, $Dstr, + (map { $posdat->{NT}{$_} || 0 } qw(A C G T N)), $Istr, $Dstr, + ) . "\n"; + # delete $data->{$chr}{$p}; + } + delete $data->{$chr}; + foreach my $r (sort { $a <=> $b } keys(%reads)) { + print QC2 join("\t", $r, $chr, $_, $amp, $reads{$r}{$_}) . "\n" foreach (sort {$a <=> $b} keys(%{$reads{$r}})); + } + print STDERR "done\n"; +} + diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/pileup2cov.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/pileup2cov.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,192 @@ +#!/usr/bin/perl -w +# + +use strict; + +my $ref = shift; +my $targets = shift; +my $fai = $ref . ".fai"; +my %idx = (); +$| = 1; +open FAI, "<$fai"; + +print STDERR "Reading fa index ... "; +while () { + chomp; + my @row = split(/\t/, $_); + $idx{$row[0]} = [@row]; +} +print STDERR "done\n"; + +close FAI; + +# Read in targets and only process alignemts if start or end is within 5bp of the primer start. +my %primes = (); +open T, "<$targets"; +while () { + my @row = split(/\t/, $_); + #456 + $primes{"$row[4]" . $_} = $row[0] foreach (($row[5] - 5) .. ($row[5] + 5), ($row[6] - 5) .. ($row[6] + 5)); +} +close T; + +open REF, "<$ref"; + +my $ppos = 0; +my $pchr = ""; +my %data = (); +my $refSeq = ""; +my $c = 0; +my $col_chr = 2; +my $col_read = 9; +my $col_qual = 10; +my $col_pos = 3; +my $col_cigar = 5; +my $refSeqPad = "P"; + +my $cnt = 1; +while () { + + # Skip stampy reads? + next unless (/XP:Z:BWA/); + + my @row = split(/\t/, $_); +# print STDERR $row[$col_pos] . "\n"; +# my $aln = ""; + if (($pchr ne $row[$col_chr])) { # flush data when chr changes or when target changes? + &flush(\%data, $pchr); + $pchr = $row[$col_chr]; + last if ($pchr eq "*"); + print STDERR "$pchr - Processing ... "; + } + my $read = $row[$col_read]; + my $qual = $row[$col_qual]; + my $pos = $row[$col_pos]; + my @cig = (); + my $aln = 0; + while ($row[$col_cigar] =~ /(\d+)(\D)/g) { + push @cig, [$1, $2]; + $aln += $1; + } + if ($ppos != $pos) { + my $offset = $idx{$row[$col_chr]}->[2]; + my $nl = int (($row[$col_pos] - 1) / $idx{$row[$col_chr]}->[3]); + $offset += $row[$col_pos] + $nl - 1; + seek REF, $offset, 0; + $refSeqPad = substr($refSeq, -1, 1); + read REF, $refSeq, 1000; # length($read) * 5; + $refSeq =~ s/\s//g; +# $data{$row[$col_chr]}{$row[$col_pos] + $_}{"refNT"} = substr($refSeq, $_, 1) foreach (0 .. (length($refSeq) - 1)); + $data{$row[$col_chr]}{$row[$col_pos] + $_}{"refNT"} = substr($refSeq, $_, 1) foreach (0 .. $aln); + $ppos = $pos; + } +# while ($row[$col_cigar] =~ /(\d+)(\D)/g) { + foreach my $cigE (@cig) { + my $n = $cigE->[0]; + if ($cigE->[1] eq "I") { +# my $insert = substr($read, 0, $1, ""); +# $data{$row[$col_chr]}{$pos}{"I"}{$insert}++; + my $rpos = $pos - $row[$col_pos]; + my $insert = substr($refSeq, $rpos - 1, 1) or print STDERR "Outside?" . $rpos . ":" . length($refSeq) . " $pos\n"; + $insert .= substr($read, 0, $n, ""); + my $qinsert .= substr($qual, 0, $n, ""); + $data{$row[$col_chr]}{$pos - 1}{"I"}{$insert}++; +# print STDERR "+"; + } + elsif ($cigE->[1] eq "M") { + my $mseq = substr($read, 0, $n, ""); + my $mqual = substr($qual, 0, $n, ""); + foreach my $nt (0 .. (length($mseq) - 1)) { + $data{$row[$col_chr]}{$pos + $nt}{"DP"}++; + my $ntq = substr($mqual, $nt, 1); + # TODO Changed from scalar to an array +# push @{$data{$row[$col_chr]}{$pos + $nt}{"NT"}{substr($mseq, $nt, 1)}}, $ntq; + $data{$row[$col_chr]}{$pos + $nt}{"NT"}{substr($mseq, $nt, 1)}++; +# print STDERR join(":", $row[$col_chr], $pos, $nt, substr($mseq, $nt, 1)) . "\n"; sleep 1; + } + $pos += $n; +# print STDERR "M"; + + } + elsif ($cigE->[1] eq "D") { +# my $rpos = $pos - $row[$col_pos]; +# my $deletion = substr($refSeq, $rpos, $1); # Substring out of string error ? +# $data{$row[$col_chr]}{$pos}{"D"}{$deletion}++; +# $pos += $1; + my $rpos = $pos - $row[$col_pos]; + my $deletion = substr($refSeq, $rpos - 1, $n + 1); # Substring out of string error ? + $data{$row[$col_chr]}{$pos - 1}{"D"}{$deletion}++; + $pos += $n; +# print STDERR "-"; + } + } +} +&flush(\%data, $pchr); + +close REF; + +sub match { + my $ref = shift; + my $seq = shift; + my $k = 5; + my $p = 0; + my @mm = (); + while (my $r = substr($$ref, $p, $k)) { + my $s = substr($$seq, $p, $k); + if ($r ne $s) { +# my $aln = ""; +# print "Mismatch!\n"; + foreach my $i (0 .. $k - 1) { + if (substr($r, $i, 1) ne substr($s, $i, 1)) { +# $aln .= "x"; + push @mm, [$p + $i, substr($r, $i, 1), substr($s, $i, 1)]; + } + else { +# $aln .= "|"; + } + } +# print $r . "\n$aln\n" . $s . "\n"; + + } + else { +# print $r . "\n" . $s . "\n"; + } + $p += $k; + } + + return \@mm; +} + +sub flush { + my $data = shift; + my $chr = shift; + return unless (exists($data->{$chr})); + print STDERR "printing ... "; + foreach my $p (sort {$a <=> $b} keys(%{$data->{$chr}})) { + my $posdat = $data->{$chr}{$p} || next; + next unless (exists($posdat->{DP})); + my $refNT = uc($posdat->{refNT}); + my @varOrd = sort { $posdat->{NT}{$b} <=> $posdat->{NT}{$a} } grep { $_ ne $refNT } keys(%{$posdat->{NT}}); + my $seqNT = join("/", @varOrd); + #my $refCNT = scalar(@{$posdat->{NT}{$refNT} || []}); + my $refCNT = $posdat->{NT}{$refNT} || 0; + my $varCNT = 0; + #$varCNT += scalar(@{$posdat->{NT}{$_}}) foreach (@varOrd); + $varCNT += $posdat->{NT}{$_} foreach (@varOrd); + my $Istr = "."; + my $Dstr = "."; + $Istr = join("|", map { $_ . ":" . $posdat->{I}{$_} } keys(%{$posdat->{I}})) if exists($posdat->{I}); + $Dstr = join("|", map { $_ . ":" . $posdat->{D}{$_} } keys(%{$posdat->{D}})) if exists($posdat->{D}); + print join("\t", $chr, $p, + $posdat->{DP} || 0, + $posdat->{refNT} || ".", + $seqNT || ".", + $refCNT, $varCNT, + #(map { scalar(@{$posdat->{NT}{$_} || []})} qw(A C G T N)), $Istr, $Dstr, + (map { $posdat->{NT}{$_} || 0 } qw(A C G T N)), $Istr, $Dstr, + ) . "\n"; +# delete $data->{$chr}{$p}; + } + delete $data->{$chr}; + print STDERR "done\n"; +} diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/plots.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/plots.R Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,46 @@ +#!/usr/bin/Rscript + +args <- commandArgs(T) +print(args[1]) +print(args[2]) +print(args[3]) + +read.delim(args[2], header=F, stringsAsFactors=F) -> qc +read.delim(args[1], header=F, stringsAsFactors=F) -> d + +#unique(unlist(strsplit(d$V3, "\\|"))) -> targets +targets <- qc$V1 +d[,7]/d[,4] * 100 -> d$pctREF +d[,8]/d[,4] * 100 -> d$pctVAR + +pdf(args[3], width=14) +for (i in targets) { + sel <- grepl(i, d$V3) + print(i) + for (c in unique(d$V1[sel])) { + csel <- d$V1 == c + print(c) + reg <- paste(range(d$V2[sel & csel]), collapse="-", sep="-") + creg <- paste(c, reg, sep=":") + print(reg) + print(creg) + plot(d[sel & csel,c(2,4)], type="l", ylim=c(0,max(d[sel & csel,4])), main=paste(i, creg, sep=" "), xlab="position", ylab="depth") + lines(d[sel & csel,c(2,7)], type="l", col=4) + lines(d[sel & csel,c(2,8)], type="l", col=2) + limP <- range(d[sel & csel,2]) + abline(v=c(limP[1], limP[1] + 150, limP[2] - 150, limP[2]),lty=4) + + plot(d[sel & csel,2], d$pctREF[sel & csel], type="l", ylim=c(0,100), main=paste(i, creg, sep=" "), xlab="position", ylab="%") + lines(d[sel & csel,2], d$pctVAR[sel & csel], type="l", col=2) + abline(h=c(1,5,10,50,90,95,99), lty=3, col=1) + abline(v=c(limP[1], limP[1] + 150, limP[2] - 150, limP[2]),lty=4) + } +} +hist(d$pctVAR[d$pctVAR < 20], breaks=40, ylim=c(0,1000)) +hist(d$pctREF[d$pctREF > 80], breaks=40, ylim=c(0,1000)) + +dev.off() + +print(summary(d$pctVAR)) + + diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/plotsPng.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/plotsPng.R Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,502 @@ +#!/usr/bin/Rscript + +args <- commandArgs(T) + +print(args[1]) # qc.ann.qual.txt +print(args[2]) # qc2.ann.qtxt +print(args[3]) # qc.targets.txt +print(args[4]) # res.txt (unfiltered) +print(args[5]) # clinvar +print(args[6]) # lociFilt +print(args[7]) # basename +options(warn=1) +print(paste("Reading", args[1], sep=" ")); +read.delim(args[1], header=T, stringsAsFactors=F) -> d +print(paste("Reading", args[2], sep=" ")); +read.delim(args[2], header=T, stringsAsFactors=F) -> d2 +print(paste("Reading", args[3], sep=" ")); +read.delim(args[3], header=T, stringsAsFactors=F) -> qc +print(paste("Reading", args[4], sep=" ")); +read.delim(args[4], header=T, stringsAsFactors=F, row.names=NULL) -> res +print(paste("Reading", args[5], sep=" ")); +read.delim(args[5], header=T, stringsAsFactors=F) -> dclin +print(paste("Reading", args[6], sep=" ")); +read.delim(args[6], header=F, stringsAsFactors=F) -> lociFilt +base <- args[7] + +# Error rate per cycle +# VAF distribution +# varDepth distribution ? +# Print coverage plots per amplicon + +tmpCP <- paste(d$X.chr, d$pos, sep=":") +tmpClin <- paste(dclin$X.chr, dclin$pos, sep=":") +tmpSnp <- paste(paste("chr", lociFilt[,1], sep=""), lociFilt[,2], sep=":") + +inClin <- tmpCP %in% tmpClin + +inSnp <- tmpCP %in% tmpSnp + +dir.create(base) +setwd(base) +#unique(unlist(strsplit(d$V3, "\\|"))) -> targets +targets <- qc[,1] +if (1) { +print("Plotting variant heatmap") +# Including off targets increases the amplicon length set at median amplicon length + 10%. +median(qc$end - qc$start) -> maxAmpLn +maxAmpLn <- ceiling(1.2 * maxAmpLn) +print(maxAmpLn) +ampHeatF <- matrix(ncol=maxAmpLn, nrow=nrow(qc)) +ampHeatR <- matrix(ncol=maxAmpLn, nrow=nrow(qc)) +#dPos <- paste(d$chr, d$pos, sep=":") +#errPos <- paste(dclin$chr, dclin$pos, sep=":") +#dPosClin <- dPos %in% errPos + +dPosClin <- !inClin & !inSnp + +for (i in 1:nrow(qc)) { + d$pos %in% qc$start[i]:qc$end[i] -> sel + poss <- d$pos[sel & !dPosClin] - qc$start[i] + 1 + poss <- poss[poss <= maxAmpLn] + ampHeatF[i, poss] <- d$nVar[sel & !dPosClin] + d$nN[sel & !dPosClin] + ampHeatR[i, poss] <- rev(d$nVar[sel & !dPosClin] + d$nN[sel & !dPosClin]) +} +png(paste(base,"heat","png", sep="."), width=960, height=480) +par(mar=c(4,4,4,2) + .1) + +ampHeatF[is.na(ampHeatF)] <- 0 +ampHeatR[is.na(ampHeatR)] <- 0 +layout(matrix(1:2, nrow=2)) +maxN <- quantile(ampHeatF, .99) +#heatmap(ampHeat) +boxplot(ampHeatF, ylim=c(0, maxN), pch=20, cex=.4, main="Non reference counts R1") +rect(150, 0, ncol(ampHeatF), maxN, col="#00000040") +boxplot(ampHeatR, ylim=c(0, maxN), pch=20, cex=.4, main="Non reference counts R2") +rect(150, 0, ncol(ampHeatR), maxN, col="#00000040") +dev.off() + +#d[,7]/d[,4] * 100 -> d$pctREF +#d[,8]/d[,4] * 100 -> d$pctVAR +d$nRef/d$dp * 100 -> d$pctREF +d$nVar/d$dp * 100 -> d$pctVAR +d$vaf <- d$nVar / (d$nVar + d$nRef) * 100 +print("Plotting ref frequencies") +png(paste(base,"raf","png", sep="."), width=480, height=480) +dref <- density(d$pctREF[!dPosClin]) +#plot(dref, ylim=range(dref$y[dref$x < 80] )) +hist(d$pctREF[!dPosClin], breaks=100, ylim=c(0, 30), col="#00000040", border=NA) +dev.off() + +print("Plotting var frequencies") +png(paste(base,"vaf","png", sep="."), width=480, height=480) +dvar <- density(d$pctVAR[!dPosClin]) +#plot(dvar, ylim=range(dvar$y[dvar$x > 20] )) +hist(d$pctVAR[!dPosClin], breaks=100, ylim=c(0, 30), col="#00000040", border=NA) +dev.off() + +# Set vaf cutoff +#q95 <- quantile(d$qScore, .95, na.rm=T) +q95 <- 20 +vs95 <- sd(d$pctVAR[!dPosClin & d$qScore < q95], na.rm=T) +v95 <- mean(d$pctVAR[!dPosClin & d$qScore < q95], na.rm=T) + vs95 * 3 + +nCall <- sum((d$pctVAR > v95) & d$qScore > q95 & !inSnp, na.rm=T) +print(nCall) +print("Plotting vaf vs q") +png(paste(base,"snv-q","png", sep="."), width=480, height=480) +plot(d$qScore, d$pctVAR, pch=20, cex=.5, main=paste("q:", q95, "-", "v:", v95, "--", "s:", nCall, sep=" ")) +abline(h=c(1,5), v=c(20,13), lty=2) +abline(v=q95, h=v95, lty=3, col=2) +points(d$qScore[d$dp < 100], d$pctVAR[d$dp < 100], pch=20, cex=1.2, col=2) +points(d$qScore[d$nVar < 10], d$pctVAR[d$nVar < 10], pch=20, cex=1, col=4) +legend(30,80, c("pass", "dp < 100", "nVar < 10"), col=c(1,2,4), pch=20) +dev.off() + +print("Plotting vaf vs q zoomed") +png(paste(base,"snv-q-zoom","png", sep="."), width=480, height=480) +plot(d$qScore, d$pctVAR, pch=20, cex=.5, xlim=c(0, 40),ylim=c(0,10)) +abline(h=c(1,5), v=c(20,13), lty=2) +abline(v=q95, h=v95, lty=3, col=2) +points(d$qScore[d$dp < 100], d$pctVAR[d$dp < 100], pch=20, cex=1.2, col=2) +points(d$qScore[d$nVar < 10], d$pctVAR[d$nVar < 10], pch=20, cex=1, col=4) +legend("topright", c("pass", "dp < 100", "nVar < 10"), col=c(1,2,4), pch=20) +dev.off() + +print("Plotting ins vs q") +d$vafI <- 0 +d$occI <- 0 +if (sum(d$ins != ".") > 0) { +png(paste(base,"ins-q","png", sep="."), width=480, height=480) +data.frame(matrix(unlist(strsplit(unlist(strsplit(as.character(d$ins[d$ins != "."]), "\\|")), ":")), ncol=2, byrow=T)) -> insDat +colnames(insDat) <- c("seq", "occ") +insDat$seq <- as.character(insDat$seq) +insDat$occ <- as.numeric(as.vector(insDat$occ)) +nchar(insDat$seq) -> insDat$ln +d$occI[d$ins != "."] <- insDat$occ +d$vafI[d$ins != "."] <- insDat$occ / d$nRef[d$ins != "."] +d$qScoreI[d$qScoreI > 1000] <- 1000 +plot(d$qScoreI, d$occI, pch=20, cex=1) +abline(h=c(10), v=c(20,13), lty=2) +# dp 500 +sel <- d$dp < 100 +points(d$qScoreI[sel], d$occI[sel], pch=20, cex=1.2, col=2) +# nVar 10 +#sel <- d$occI < 10 +#points(d$qScoreI[sel], d$occI[sel], pch=20, cex=1, col=3) +# vaf < 0.01 +sel <- d$vafI < 0.01 +points(d$qScoreI[sel], d$occI[sel], pch=20, cex=1, col=4) +legend("topleft", c("pass", "dp < 100", "vaf < 0.01"), col=c(1,2,4), pch=20) +dev.off() +} + +print("Plotting del vs q") +d$vafD <- 0 +d$occD <- 0 +if (sum(d$del != "." ) > 0) { +png(paste(base,"del-q","png", sep="."), width=480, height=480) +data.frame(matrix(unlist(strsplit(unlist(strsplit(as.character(d$del[d$del != "."]), "\\|")), ":")), ncol=2, byrow=T)) -> delDat +colnames(delDat) <- c("seq", "occ") +delDat$seq <- as.character(delDat$seq) +delDat$occ <- as.numeric(as.vector(delDat$occ)) +nchar(delDat$seq) -> delDat$ln +d$occD[d$del != "."] <- delDat$occ +d$vafD[d$del != "."] <- d$occD[d$del != "."] / d$nRef[d$del != "."] +d$qScoreD[d$qScoreD > 1000] <- 1000 +#hist(d$qScoreD, breaks=1000, ylim=c(0,100)) +#print(sum(d$qScoreD > 20)) +#Sys.sleep(1) +plot(d$qScoreD, d$occD, pch=20, cex=1) +abline(h=c(10), v=c(20,13), lty=2) +# dp 500 +sel <- d$dp < 100 +points(d$qScoreD[sel], d$occD[sel], pch=20, cex=1.2, col=2) +# nVar 10 +#sel <- d$occD < 10 +#points(d$qScoreD[sel], d$occD[sel], pch=20, cex=1, col=3) +# vaf < 0.01 +sel <- d$vafD < 0.01 +points(d$qScoreD[sel], d$occD[sel], pch=20, cex=1, col=4) +legend("topleft", c("pass", "dp < 100", "vaf < 0.01"), col=c(1,2,4), pch=20) +dev.off() +} + +sub("chr", "", qc$chr) -> qc$chrn +ampOrd <- order(qc$chrn, qc$start) + +print("Plotting amplicon depths") +png(paste(base,"amp-dp","png", sep="."), width=960, height=480) +barplot(qc$depth[ampOrd]) +abline(h=100, lty=2) +totRead <- sum(qc$depth, na.rm=T) +legend("topright", paste("Total read count: ", totRead, sep="")) +dev.off() +} +# +res$POS <- as.numeric(as.vector(res$POS)) +d$pos <- as.numeric(as.vector(d$pos)) + +grepl("a", d$ntRef, ignore.case=T) -> Asel +grepl("c", d$ntRef, ignore.case=T) -> Csel +grepl("g", d$ntRef, ignore.case=T) -> Gsel +grepl("t", d$ntRef, ignore.case=T) -> Tsel +cntr <- 0 + +biasTable <- data.frame(matrix(NA, nrow=length(targets), ncol=12), row.names=targets) +colnames(biasTable) <- c("AC", "AG", "AT", "CA", "CG", "CT", "GA", "GC", "GT", "TA", "TC", "TG") + +for (i in targets) { + sel <- grepl(i, d$amp) + print(i) + for (c in unique(d[sel,1])) { + csel <- d[,1] == c + print(c) + reg <- paste(range(d[sel & csel,2]), collapse="-", sep="-") + creg <- paste(c, reg, sep=":") + + qcsel <- qc[,1] == i + allsel <- sel & csel + clinSel <- dclin$amp == i + clinPos <- dclin$pos[clinSel] +# inClin <- d$pos %in% clinPos + + #dels <- (d[,15] != ".") & allsel + #ins <- (d[,14] != ".") & sel + # print(reg) + # print(creg) + + # Select annotations + # calculate quantiles and plot them +# quantile(d$pctVAR[sel & csel], c(.75,.90,.95,.99), na.rm=T) -> cutoffs + tmp <- d[sel & csel,] + #dels <- tmp[,15] != "." + #ins <- tmp[,14] != "." + dels <- allsel & d$del != "." + ins <- allsel & d$ins != "." + + resTmp <- res[(res$POS >= min(tmp[,2])) & (res$POS <= max(tmp[,2])) & (res$X.CHROM == c),] + #resSel <- res$TARGET == i + png(paste(base, i, "cov", "png", sep="."), width=960, height=480) + + xvec <- c(0, rep(1:(sum(allsel) - 1), each=2), sum(allsel)) + layout(matrix(1:2, ncol=1), heights=c(2,1)) + par(mar=c(0, 4, 4, 7) + .1, xaxt="n") + print("Cov") + plot(NULL, type="n", main=i, xlab="Position", ylab="Depth", xlim=range(d$pos[allsel]), ylim=range(0, d$dp[allsel])) + xvec <- d$pos[allsel] + yvec <- d$dp[allsel] + + polygon(rep(c(xvec, max(xvec) + 1), each=2) - .5, c(0, rep(yvec, each=2), 0), col="#00000010", border=1) + polygon(rep(c(xvec, max(xvec) + 1), each=2) - .5, c(0, rep(rowSums(d[allsel, 7:8]), each=2), 0), col="#00000010") +# polygon(rep(c(xvec, max(xvec) + 1), each=2) - .5, c(0, rep(d$nVar[allsel], each=2), 0), col=2) + varCol <- rep(2, sum(allsel)) + varCol[grepl("^a", d$ntVar[allsel], ignore.case=T)] <- "green" + varCol[grepl("^c", d$ntVar[allsel], ignore.case=T)] <- "blue" + varCol[grepl("^g", d$ntVar[allsel], ignore.case=T)] <- "black" + varCol[grepl("^t", d$ntVar[allsel], ignore.case=T)] <- "red" + rect(xvec-.5,d$nVar[allsel],xvec+.5,0, col=varCol) + + + ampMax <- max(d[allsel,4]) + #abline(v=resTmp$POS, lty=2, col=2) + #delMark <- list() + #insMark <- list() + + for (idx in which(dels)) { + matrix(unlist(strsplit(as.character(as.vector(d[idx,15])), "[:|]")), ncol=2, byrow=T) -> delDat + nchar(delDat[,1]) -> lngts + dpths <- as.numeric(delDat[,2]) + x1 <- d[idx,2] + .5 + x2 <- x1 + lngts - 1 + if (x2 > max(d$pos[allsel])) { + next + } + # delMark[[length(delMark) + 1]] <- c(x1, x2) + rect(x1, ampMax - dpths , x2, ampMax, col="#00000040") + } + + for (idx in which(ins)) { + matrix(unlist(strsplit(as.character(as.vector(d[idx,14])), "[:|]")), ncol=2, byrow=T) -> insDat + nchar(insDat[,1]) -> lngts + dpths <- as.numeric(insDat[,2]) + x1 <- d$pos[idx] + 1 + # insMark[length(insMark) + 1] <- x1 + for (ii in 1:ncol(insDat)) { + polygon( + c(x1, x1 - (.5 * lngts[ii]), x1 + (.5 * lngts[ii])), + c(ampMax, ampMax - dpths[ii], ampMax - dpths[ii]), + , col="#00000040") + } + } + par(xpd=NA) + legend(max(d$pos[allsel]) + sum(allsel) * 0.05, ampMax, legend=c("Filtered nt", "Ref nt", "Non-ref nt"), col=c("#00000040", "#00000080", "red"), pch=15) + legend(max(d$pos[allsel]) + sum(allsel) * 0.05, 0, legend=c("A", "C", "G", "T"), col=c("green", "blue", "black", "red"), pch=15) + par(xpd=F) + par(mar=c(5, 4, 0, 7) + .1, xaxt="s") + plot(NULL, type="n", xlab="Position", ylab=NA, xlim=range(d$pos[allsel]), ylim=c(0,4.5), yaxt="n") + axis(side=2, at=1:4, labels=c("ins", "del", "snv", "ref"), las=2) + abline(h=1:4, col="#00000040") + sres <- nchar(as.character(resTmp$REF)) == nchar(as.character(resTmp$ALT)) + dres <- nchar(resTmp$REF) > nchar(resTmp$ALT) + ires <- nchar(resTmp$REF) < nchar(resTmp$ALT) + + resTmp$marks <- rep(3.4, nrow(resTmp)) + + resTmp$cols <- rep("#00000040", nrow(resTmp)) + resTmp$cols[grepl("^a", resTmp$ALT, ignore.case=T) & sres] <- "green" + resTmp$cols[grepl("^c", resTmp$ALT, ignore.case=T) & sres] <- "blue" + resTmp$cols[grepl("^g", resTmp$ALT, ignore.case=T) & sres] <- "black" + resTmp$cols[grepl("^t", resTmp$ALT, ignore.case=T) & sres] <- "red" + + #resTmp$cols[dres] <- 2 + #resTmp$cols[ires] <- 2 + resTmp$marks[dres] <- 2.4 + resTmp$marks[ires] <- 1.4 + resTmp$markP1 <- resTmp$POS -.5 + resTmp$markP2 <- resTmp$POS +.5 + resTmp$markP1[dres] <- resTmp$POS[dres] +.5 + resTmp$markP2[dres] <- resTmp$POS[dres] +.5 + nchar(resTmp$REF[dres]) - 1 + resTmp$markP1[ires] <- resTmp$POS[ires] +.5 + resTmp$markP2[ires] <- resTmp$POS[ires] +.5 + 1 + ntCol <- rep(1, sum(allsel)) + ntCol[grepl("a", d$ntRef[allsel], ignore.case=T)] <- "green" + ntCol[grepl("c", d$ntRef[allsel], ignore.case=T)] <- "blue" + ntCol[grepl("g", d$ntRef[allsel], ignore.case=T)] <- "black" + ntCol[grepl("t", d$ntRef[allsel], ignore.case=T)] <- "red" + + rect(d$pos[allsel] -.5, 4.4, d$pos[allsel] +.5, 3.6, col=ntCol, border=0) + rect(resTmp$markP1, resTmp$marks, resTmp$markP2, resTmp$marks - .8, col=resTmp$cols, border=0) + + if(length(clinPos != 0)) { + rect(clinPos - .5, 3.5, clinPos + .5, .5, border="black", lwd=2) + } + #lapply(delMark, function(x) { rect(x[1], 2, x[2], 1, col=2, border=NA) }) + #lapply(insMark, function(x) { rect(x[1], 1, x[1] + 1, 0, col=3, border=NA) }) + + # Highlight clinically relevant loci + #for (i in which(dclin$amp == i)) { + # if (dclin$REF[i] == nchar + #} + + dev.off() + + sansClin <- allsel & !inClin + sansSnp <- allsel & !inSnp + + d$nA[sansClin & sansSnp & Asel] -> AA + d$nC[sansClin & sansSnp & Asel] -> AC + d$nG[sansClin & sansSnp & Asel] -> AG + d$nT[sansClin & sansSnp & Asel] -> AT + + d$nA[sansClin & sansSnp & Csel] -> CA + d$nC[sansClin & sansSnp & Csel] -> CC + d$nG[sansClin & sansSnp & Csel] -> CG + d$nT[sansClin & sansSnp & Csel] -> CT + + d$nA[sansClin & sansSnp & Gsel] -> GA + d$nC[sansClin & sansSnp & Gsel] -> GC + d$nG[sansClin & sansSnp & Gsel] -> GG + d$nT[sansClin & sansSnp & Gsel] -> GT + + d$nA[sansClin & sansSnp & Tsel] -> TA + d$nC[sansClin & sansSnp & Tsel] -> TC + d$nG[sansClin & sansSnp & Tsel] -> TG + d$nT[sansClin & sansSnp & Tsel] -> TT + + print("Bias") + png(paste(base, i, "bias", "png", sep="."), width=960, height=480) + + Acnt <- sum(sum(AA), sum(AC), sum(AG), sum(AT)) + Ccnt <- sum(sum(CA), sum(CC), sum(CG), sum(CT)) + Gcnt <- sum(sum(GA), sum(GC), sum(GG), sum(GT)) + Tcnt <- sum(sum(TA), sum(TC), sum(TG), sum(TT)) + + NTsums <- c( + sum(AC)/Acnt, sum(AG)/Acnt, sum(AT)/Acnt, + sum(CA)/Ccnt, sum(CG)/Ccnt, sum(CT)/Ccnt, + sum(GA)/Gcnt, sum(GC)/Gcnt, sum(GT)/Gcnt, + sum(TA)/Tcnt, sum(TC)/Tcnt, sum(TG)/Tcnt) + NTsums[!is.finite(NTsums)] <- 0 + NTsums[is.nan(NTsums)] <- 0 + NTsums[is.na(NTsums)] <- 0 + + barplot(NTsums, names.arg=c("AC", "AG", "AT", "CA", "CG", "CT", "GA", "GC", "GT", "TA", "TC", "TG"), main=i) + dev.off() + biasTable[rownames(biasTable) == i, ] <- NTsums + + print("Cov2") + png(paste(base, i, "cov2", "png", sep="."), width=960, height=480) + layout(matrix(1:2, ncol=1), heights=c(2,1)) + par(mar=c(0, 4, 4, 7) + .1, xaxt="n") + + + dat <- d2[d2$amp == i,] + rled <- rle(sort(dat$pos)) + rds <- sort(unique(dat$X.read)) + lst <- c() + for (ii in order(rled$lengths, decreasing=T)) + { + + rled$values[ii] -> pos + dat$X.read[dat$pos == pos] + lst <- c(lst, rds %in% dat$X.read[dat$pos == pos]) + + } + #xlim <- range(dat$pos) + xlim=range(d$pos[allsel]) + ylim=range(0, d$dp[allsel]) + plot(NULL, xlim=xlim, ylim=ylim, main=i, ylab="Depth") + rect(xlim[1] - 0.5, 0, xlim[2] + .5, ylim[2], col="#00000010") + if (length(lst) > 0) { + matrix(lst, nrow=length(rds), byrow=F) -> mat + do.call( order, data.frame(mat) ) -> ord + for (e in 1:length(ord)) { + sel <- dat$X.read == rds[ord[e]] + colvec <- rep(1, sum(sel)) + colvec[grepl("A$", dat$event[sel], ignore.case=T)] <- "green" + colvec[grepl("C$", dat$event[sel], ignore.case=T)] <- "blue" + colvec[grepl("G$", dat$event[sel], ignore.case=T)] <- "black" + colvec[grepl("T$", dat$event[sel], ignore.case=T)] <- "red" + #points(dat$pos[ sel ], rep(e, sum(sel)), col=colvec, pch=20, cex=.2) + segments(dat$pos[ sel ] - .5, rep(e, sum(sel)), dat$pos[ sel ] + .5, rep(e, sum(sel)), col=colvec, pch=20, cex=.2) + } + } + + par(xpd=NA) + legend(max(d$pos[allsel]) + sum(allsel) * 0.05, ampMax, legend=c("Filtered nt", "Ref nt", "Non-ref nt"), col=c("#00000040", "#00000080", "red"), pch=15) + legend(max(d$pos[allsel]) + sum(allsel) * 0.05, 0, legend=c("A", "C", "G", "T"), col=c("green", "blue", "black", "red"), pch=15) + par(xpd=F) + par(mar=c(5, 4, 0, 7) + .1, xaxt="s") + plot(NULL, type="n", xlab="Position", ylab=NA, xlim=range(d$pos[allsel]), ylim=c(0,4.5), yaxt="n") + axis(side=2, at=1:4, labels=c("ins", "del", "snv", "ref"), las=2) + abline(h=1:4, col="#00000040") + sres <- nchar(as.character(resTmp$REF)) == nchar(as.character(resTmp$ALT)) + dres <- nchar(resTmp$REF) > nchar(resTmp$ALT) + ires <- nchar(resTmp$REF) < nchar(resTmp$ALT) + + resTmp$marks <- rep(3.4, nrow(resTmp)) + + resTmp$cols <- rep("#00000040", nrow(resTmp)) + resTmp$cols[grepl("^a", resTmp$ALT, ignore.case=T) & sres] <- "green" + resTmp$cols[grepl("^c", resTmp$ALT, ignore.case=T) & sres] <- "blue" + resTmp$cols[grepl("^g", resTmp$ALT, ignore.case=T) & sres] <- "black" + resTmp$cols[grepl("^t", resTmp$ALT, ignore.case=T) & sres] <- "red" + + #resTmp$cols[dres] <- 2 + #resTmp$cols[ires] <- 2 + resTmp$marks[dres] <- 2.4 + resTmp$marks[ires] <- 1.4 + resTmp$markP1 <- resTmp$POS -.5 + resTmp$markP2 <- resTmp$POS +.5 + resTmp$markP1[dres] <- resTmp$POS[dres] +.5 + resTmp$markP2[dres] <- resTmp$POS[dres] +.5 + nchar(resTmp$REF[dres]) - 1 + resTmp$markP1[ires] <- resTmp$POS[ires] +.5 + resTmp$markP2[ires] <- resTmp$POS[ires] +.5 + 1 + ntCol <- rep(1, sum(allsel)) + ntCol[grepl("a", d$ntRef[allsel], ignore.case=T)] <- "green" + ntCol[grepl("c", d$ntRef[allsel], ignore.case=T)] <- "blue" + ntCol[grepl("g", d$ntRef[allsel], ignore.case=T)] <- "black" + ntCol[grepl("t", d$ntRef[allsel], ignore.case=T)] <- "red" + + rect(d$pos[allsel] -.5, 4.4, d$pos[allsel] +.5, 3.6, col=ntCol, border=0) + rect(resTmp$markP1, resTmp$marks, resTmp$markP2, resTmp$marks - .8, col=resTmp$cols, border=0) + + if(length(clinPos != 0)) { + rect(clinPos - .5, 3.5, clinPos + .5, .5, border="black", lwd=2) + } + + + dev.off() + +# png(paste(base, i, "vaf", "png", sep="."), width=960, height=480) +# plot(d[sel & csel,2], d$vaf[sel & csel], type="l", ylim=c(0,100), main=paste(i, creg, cutoffs[3], sep=" "), xlab="position", ylab="%", col=2) + #lines(d[sel & csel,2], d$pctVAR[sel & csel], type="l", col=2) +# abline(h=100) +# abline(h=c(1,5,10,50,90,95,99), lty=3, col=1) +# abline(h=cutoffs[3], lty=4, col=2) +# abline(v=c(limP[1], limP[1] + 150, limP[2] - 150, limP[2]),lty=4) +# abline(v=c(qc[qcsel,8:9]), lty=5, col=2) +# if (length(labs != 0)) { +# text(resTmp$POS[resTmp$vaf > (cutoffs[3]/100)], 50, labels=resTmp$Amino_Acid_change[resTmp$vaf > (cutoffs[3]/100)]) +# abline(v=resTmp$POS[resTmp$vaf > (cutoffs[3]/100)], col="grey", lty=4) +# } +# dev.off() + } +} + +png(paste(base, "biasheat", "png", sep="."), width=960, height=960) +write.table(biasTable, paste(base, "bias", "tsv", sep="."), sep="\t") +biasTable[is.na(biasTable)] <- 0 +heatmap(data.matrix(biasTable), Colv=NA, scale="r") +dev.off() +png(paste(base, "bias", "png", sep="."), width=960, height=480) +boxplot(data.matrix(biasTable), pch=20, cex=.5) +dev.off() +warnings() +#hist(d$pctVAR[d$pctVAR < 20], breaks=40, ylim=c(0,1000)) +#hist(d$pctREF[d$pctREF > 80], breaks=40, ylim=c(0,1000)) + +#print(summary(d$pctVAR)) + + diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/plotsQC.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/plotsQC.R Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,51 @@ +#!/usr/bin/Rscript + +args <- commandArgs(T) +print(args[1]) +print(args[2]) + +read.delim(args[1], header=F, stringsAsFactors=F) -> alnStats +read.delim(args[2], header=F, stringsAsFactors=F) -> errStats + +library(RColorBrewer) +#cols <- brewer.pal(3, "Blues") +cols <- c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7") + +xlegend <- 1.2 * nrow(alnStats) * 1.15 +png("alnStats.png", width=960, height=480, res=72) + +alnStats[,2:5] / 1000000 -> alnStats[,2:5] +fair <- mean(alnStats[,2]) +sub(".bam$", "", alnStats[,1]) -> alnStats[,1] +sub(".qc.ann.txt$", "", errStats[,1]) -> errStats[,1] + +oldMar <- par()$mar +par(mar=c(8.1, 4.1, 4.1, 6.1), xpd=T) +barplot(as.matrix(t(alnStats[order(alnStats[,1]),c(3:5)])), names.arg=alnStats[order(alnStats[,1]),1], las=3, col=cols[1:3], main="Alignment efficiency", ylab="Reads (Millions)", legend.text=c("Ontarget", "Offtarget", "Unmapped"), angle=.5, args.legend=c(x=xlegend)) +par(xpd=F) +abline(h=fair, lty=2) +dev.off() + +png("errStats.png", width=960, height=480, res=72) +par(mar=c(8.1, 4.1, 4.1, 6.1)) +barplot(errStats$V4[order(errStats[,1])], names.arg=errStats[order(errStats[,1]),1], las=3, col=cols[1], main="Error rate", ylab="%") + +abline(h=1, lty=2) +dev.off() + +png("qualStats.png", width=960, height=480, res=72) +par(mar=c(8.1, 4.1, 4.1, 6.1), xpd=T) +barplot(as.matrix(t(alnStats[order(alnStats[,1]),c(6:9)])), names.arg=alnStats[order(alnStats[,1]),1], las=3, col=cols[1:4], main="Quality stats", ylab="%", legend.text=c("Q > 30", "30 < Q >= 20", "20 < Q >= 10", "Q < 10"), angle=.5, args.legend=c(x=xlegend)) +dev.off() + + +#library(ggplot2) +#png("alnStatsgg.png", width=960, height=480, res=72) +#df <- data.frame( +# sample= c(rep(alnStats[,1], 3)), +# target = c(rep("ontarget", nrow(alnStats)), rep("offtarget", nrow(alnStats)), rep("unmapped", nrow(alnStats))), +# count = c(alnStats[,3], alnStats[,4], alnStats[,5]) +#) +# +#ggplot(data=df, aes(x=sample, y=count, fill=target)) + geom_bar(stat="identity") +#dev.off() diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/qc2vcf.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/qc2vcf.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,135 @@ +#!/usr/bin/perl + +use strict; + +my $qc = shift; + +my $minDp = 100; +my $minVarDp = 5; +my $minVaf = 0.01; + +my $base = (split(/\//, $qc))[-1]; +my $header = qq(##fileformat=VCFv4.1 +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT $base +); + +my $chr = 0; +my $pos = 1; +my $target = 2; +my $dp = 3; +my $ref = 4; +my $var = 5; +my $nref = 6; +my $nvar = 7; +my $nA = 8; +my $nC = 9; +my $nG = 10; +my $nT = 11; +my $nN = 12; +my $ins = 13; +my $del = 14; +my $pval = 15; +my $pvala = 16; +my $varQual = 17; +my $insQual = 18; +my $delQual = 19; + +my %acgt = (A => 0, C => 1, G => 2, T => 3); +print $header; +open QC, "<$qc"; +while () { + chomp; + next if (/^#/); + next if (/^X\./); + my @row = split(/\t/, $_); + next if ($row[$target] eq "."); + + my $VAR = substr($row[$var], 0, 1); + my $REF = $row[$ref]; + my $nvarall = $row[$nvar]; + my $indel = $row[$ins] . $row[$del]; + if ($row[$nvar] > 0 || $indel eq "..") { + my %ord = ( A => $row[$nA], C => $row[$nC], G => $row[$nG], T => $row[$nT], N => $row[$nN] ); + $ord{uc($REF)} = -1; # Exclude ref from sort + $ord{N} = -1; # Exclude N! + my @order = sort { $ord{$b} <=> $ord{$a} } keys(%ord); + my $dpVar = $ord{$order[0]}; + my $VAR = $order[0]; + my $skip = 0; + my $tot = $row[$nref] + $dpVar; + my $vaf = ($tot > 0)?$dpVar / $tot:"NA"; # Excluding other alleles... + #$skip++ if ($tot == 0); + #$skip++ if ($ord{$order[0]} == $ord{$order[1]}); # Multiallelic, skipping for now + #$skip++ if ($dpVar == 0); # Skip if dpVar is zero, can occur when N is the only variant. Above line also protects for this. + #$skip++ if ($dpVar < $minVarDp); + #$skip++ if ($row[$dp] < $minDp); + #$skip++ if ($vaf < $minVaf); + my $gt = "$row[$ref]/$VAR"; + my $qual = $row[$varQual] || 0; + $skip++ if ($qual == 0); + my $filter = 0; + my $info = "TARGET=$row[$target]"; + my $format = "DP:AD:AB"; + my $sample = "$row[$dp]:$row[$nref],$dpVar:$vaf"; + print join("\t", @row[$chr, $pos], ".", $REF, $VAR, $qual, $filter, $info, $format, $sample) . "\n" if ($skip == 0); + } + # INDEL + if ($row[$ins] ne ".") { + my $skip = 0; + # Modify coordinte to conform to VCF? + my %inss = split(/[\|\:]/, $row[$ins]); + my @keys = sort { $inss{$b} <=> $inss{$a} } keys %inss; +# if ($inss{$keys[0]} > $row[$nvar]) { +# $nvarall = $inss{$keys[0]}; +# $VAR = $keys[0]; +# $row[$dp] += $nvarall; +# } + my $nins = $inss{$keys[0]}; + my $DP = $row[$dp]; + my $nREF = $DP - $nins; + #$skip++ if ($nins < $minVarDp); + #$skip++ if ($DP < $minDp); + my $vaf = $nins / $row[$dp]; + #$skip++ if ($vaf < $minVaf); + my $gt = "$row[$ref]/$keys[0]"; + my $qual = $row[$insQual]; + $skip++ if ($qual == 0); + my $filter = 0; + my $info = "TARGET=$row[$target]"; + my $format = "DP:AD:AB"; + my $sample = "$DP:$nREF,$nins:$vaf"; + print join("\t", @row[$chr, $pos], ".", $REF, $keys[0], $qual, $filter, $info, $format, $sample) . "\n" if ($skip == 0); + } + if ($row[$del] ne ".") { + my $skip = 0; + # Modify coordinte to conform to VCF? + my %dels = split(/[\|\:]/, $row[$del]); + my @keys = sort { $dels{$b} <=> $dels{$a} } keys %dels; +# if ($dels{$keys[0]} > $row[$nvar]) { +# $nvarall = $dels{$keys[0]}; +# $REF = $keys[0]; +# $row[$dp] += $nvarall; +# } + my $ndel = $dels{$keys[0]}; + my $DP = $row[$dp]; + my $nREF = $DP - $ndel; + #$skip++ if ($ndel < $minVarDp); + #$skip++ if ($DP < $minDp); + my $vaf = $ndel / $DP; + #$skip++ if ($vaf < $minVaf); + my $gt = "$keys[0]/$row[$ref]"; + my $qual = $row[$delQual]; + $skip++ if ($qual == 0); + my $filter = 0; + my $info = "TARGET=$row[$target]"; + my $format = "DP:AD:AB"; + my $sample = "$DP:$nREF,$ndel:$vaf"; + print join("\t", @row[$chr, $pos], ".", $keys[0], $row[$ref], $qual, $filter, $info, $format, $sample) . "\n" if ($skip == 0); + } +} +close QC; + diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/qcFilt.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/qcFilt.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,93 @@ +#!/usr/bin/perl + +use strict; + +my $qcQual = shift; +my $clinvar = shift; +my $cosmic = shift; +my $cosmicNC = shift; +my $output = shift; + +my $minDp = shift || 100; +my $minVar = shift || 10; +my $minIns = shift || $minVar; +my $minDel = shift || $minVar; +my $minVarQ = shift || 100; +my $minInsQ = shift || 200; +my $minDelQ = shift || 200; + +my %cvHsh = (); +print STDERR "Reading clinvars...\n"; +open CV, "<$clinvar"; +while () { last if (/#CHROM/); } +while () { + chomp; + my @row = split(/\t/, $_); + $cvHsh{"chr".$row[0].":".$row[1]} = [@row]; +} +close CV; + +print STDERR "Reading COSMIC...\n"; +open CV, "<$cosmic"; +while () { last if (/#CHROM/); } +while () { + chomp; + my @row = split(/\t/, $_); + $cvHsh{"chr".$row[0].":".$row[1]} = [@row]; +} +close CV; + +print STDERR "Reading COSMICNC...\n"; +open CV, "<$cosmicNC"; +while () { last if (/#CHROM/); } +while () { + chomp; + my @row = split(/\t/, $_); + $cvHsh{"chr".$row[0].":".$row[1]} = [@row]; +} + +close CV; +print STDERR "done!"; + +open QC, "<$qcQual"; +my $head = readline QC; +chomp; +$head =~ s/\s+$//; +my @rhead = split(/\t/, $head); +my $coln = 0; +my %col = map { $_ => $coln++ } @rhead; +open OUT, ">$output.qc.ann.qual.filt.txt"; +open CVOUT, ">$output.qc.ann.qual.clinvar.txt"; +print OUT "$head\n"; +print CVOUT "$head\n"; + +while () { + my $line = $_; + my @row = split(/\t/, $_); + my $key = $row[$col{"X.chr"}] . ":" . $row[$col{pos}]; + if (exists($cvHsh{$key})) { + print CVOUT $line; + } + next if ($row[$col{dp}] < $minDp); + # Var + if ($row[$col{qScore}] >= $minVarQ && $row[$col{nVar}] > $minVar) { + print OUT $line; + } + # Ins + if ($row[$col{qScoreI}] >= $minInsQ) { + $row[$col{ins}] =~ /:(\d+)/; + if ($1 >= $minIns) { + print OUT $line; + } + } + # Del + if ($row[$col{qScoreD}] >= $minDelQ) { + $row[$col{del}] =~ /:(\d+)/; + if ($1 >= $minDel) { + print OUT $line; + } + } +} + +close OUT; +close CVOUT; diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/report.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/report.sh Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,24 @@ +#!/bin/bash + +DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" + +base=$1 + +vcf2tsv=$DIR/../../misc/vcf2tsv.pl +spliteff=$DIR/splitEff.pl +addQc=$DIR/addQc.pl +filter=$DIR/filter.pl + +# convert to tsv +$vcf2tsv $base.samtools.vcf > $base.samtools.tsv +$vcf2tsv $base.vs.snp.a.vcf > $base.vs.snp.a.tsv + +# split eff columns +$spliteff $base.samtools.tsv > $base.res.tmp +$spliteff $base.vs.snp.a.tsv >> $base.res.tmp + +# add count data +$addQc $base.res.tmp $base.qc.ann.txt > $base.res.tsv + +# Filter +$filter $base.res.tsv > $base.res.filtered.tsv diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/splitEff.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/splitEff.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,82 @@ +#!/usr/bin/perl -w +# +use strict; +my $file = shift; +my $tag = shift || "NoTag"; + +open F, "<$file"; +my $head = undef; +my %effIdx = (); +$effIdx{context} = 0; +while () { + if (/.*ID=EFF.*($.*$).*/) { + my $str = $1; +# print STDERR $str . "\n"; + $str =~ s/\[.*\]//g; +# print STDERR $str . "\n"; + $str =~ s/^$\s*(.*?)\s*$$/$1/; +# print STDERR $str . "\n"; + my $c = 1; + $effIdx{lc($_)} = $c++ foreach split(/\s*\|\s*/, $str); +# print STDERR join("\n", map { $_ . ":" . $effIdx{$_} } keys(%effIdx)) . "\n"; +# exit; + } + if (/#CHROM/) { + $head = $_; + last; + } + +} + +chomp $head; +my @hrow = split(/\t/, $head); +my $colN = 0; +#my %col = map { print STDERR "$_ => $colN\n";$_ => $colN++ } @hrow; +my %col = map { $_ => $colN++ } @hrow; +# Add AD column +# Convert DP4 for samtools file +my $ADName = (grep { /\_AD/ } keys(%col))[0]; +if (exists($col{DP4})) { + $ADName = "DP4"; +} +my $ADCol = $col{$ADName}; + +my $DPName = (grep { /\_DP/ } keys(%col))[0]; +if (exists($col{DP})) { + $DPName = "DP"; +} +my $DPCol = $col{$DPName}; + +#print STDERR $ADName . "\t" . $col{$ADName} . " $ADCol\n"; + +#Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] ) +my @Col = qw/DP AD Context Effect_Impact Functional_Class Codon_Change Amino_Acid_change Amino_Acid_length Gene_Name Transcript_BioType Gene_Coding Transcript_ID Exon_Rank Tag/; + +my @effCol = map {lc} qw/Context Effect_Impact Functional_Class Codon_Change Amino_Acid_change Amino_Acid_length Gene_Name transcript_BioType Gene_Coding Transcript_ID Exon_Rank/; +my @effColOrd = map {$effIdx{$_}} @effCol; + +print join("\t", @hrow[0 ..5], @Col) . "\n"; #map { "eff$_" } 1 .. 10) . "\n"; +while () { + chomp; + my @row = split(/\t/, $_); + + if ($ADName eq "DP4") { + my @dp4row = split(/,/, $row[$ADCol]); +# print STDERR join(":", @dp4row) . "\n"; sleep 1; + $row[$ADCol] = ($dp4row[0] + $dp4row[1]) . "," . ($dp4row[2] + $dp4row[3]); + } + +# print $row[$col{EFF}] . "\n"; + my @effs = split(/,/, $row[$col{EFF}]); + foreach my $eff (@effs) { + $eff =~ s/\)$//; + my @effrow = split(/[\|]/, $eff, -1); + +# print STDERR scalar(@effrow) . " $eff\n"; +# print STDERR join(":", @effrow) . " $eff\n"; sleep 1; + print join("\t", @row[0 .. 5, $DPCol, $ADCol], @effrow[@effColOrd], $tag) . "\n"; + + } +} + +close F; diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/startAnalysis.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/startAnalysis.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,94 @@ +#!/usr/bin/perl -w + +use strict; +use Sys::Hostname; + +my $dir = shift || undef; +my $tMax = shift || 2; +my $binDir = "/ccagc/lib/pipelines/TSACP/falco/"; +#my $binDir = "/ccagc/lib/daoud/AAP/amplicon-analysis-pipeline/"; +my @files = (); +my %pairs = (); +#if ($#ARGV == -1) { + +unless (-d $dir) { + &stderr($dir . " not found"); + exit; +} + +if ($dir) { + chdir $dir; + open FILES, "find -L ./ -iname \"*fastq.gz\"|"; + while () { + chomp; + push @files, $_; + } +} +else { + while () { + chomp; + push @files, $_; + } +} + +if ($#files == -1) { + &stderr("No fastq found, exiting"); + exit; +} + +foreach my $f (@files) { + chomp $f; + $f =~ /^(.*)\/(.*)_(.*?)_(.*?)_(.*?)_(.*?)$/; + next if ($3 =~ /Undetermined/); + #print $2 . " $f\n"; + $pairs{$2}{$5} = $f; + +} +my $bin = "$binDir/amplicon-Al-TSACP.sh"; +my $dstamp = `date +"%y%m%d"`; +my $tCnt = 0; +my %pidHsh = (); +#print STDERR "PID $$\n"; +&stderr("PID $$"); +foreach my $pair (keys(%pairs)) { + next if ($pair =~ /Undetermined/); + my $pid = fork; + print "$$ $pid \n"; + sleep 1; + if ($pid) { + $pidHsh{$pid} = localtime(); +# print STDERR localtime() . " : Forking $pid : $pair\n"; + &stderr("Forking $pid : $pair"); + while (scalar(keys(%pidHsh)) >= $tMax) { + my $deceased = wait; + #print STDERR localtime() . " : $deceased $pidHsh{$deceased} finished\n" if (exists($pidHsh{$deceased})); + &stderr("$deceased $pidHsh{$deceased} finished") if (exists($pidHsh{$deceased})); + delete($pidHsh{$deceased}); + } + sleep 1; + } + else { +# print STDERR localtime() . " : Child $$ forked??\n"; + &stderr("Child $$ forked"); + system("$bin $pairs{$pair}{R1} $pairs{$pair}{R2} $pair > $pair.log 2>&1"); + &stderr("Child $$ done"); + exit; + #print STDERR localtime() . " : Child $$ I should be dead by now,...\n"; + } +} + +1 while (wait() != -1); + +my $bin2 = "$binDir/amplicon-QC.sh"; +#print STDERR localtime() . " : Generating run QC $bin2\n"; +&stderr("Generating run QC $bin2"); +system($bin2); +my $bin3 = "$binDir/misc/mkHtmlReport.pl ./ ./"; +#print STDERR localtime() . " : Generating HTML $bin3\n"; +&stderr("Generating HTML $bin3"); +system($bin3); + +sub stderr { + my $msg = shift; + print STDERR localtime() . " [" . hostname . "] [$$] : $msg\n"; +} diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/varFilter.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/varFilter.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,83 @@ +#!/usr/bin/perl +# +# Take target regions and call variants based on simple depth en frequency thresholds + +my $minDepth = shift || 100; +my $minFreq = shift || 0.01; +my $minVar = shift || 10; + +my $depthCol = 3; +my $varCol = 7; +my %nt = ( + A => 8, + C => 9, + G => 10, + T => 11, +); +my $input = shift; +my $fh = undef; +if (defined $input) { + open ($fh, "<$input"); +} +else { + $fh = *STDIN unless (defined $fh); +} + +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Mutant25 +my $prevNT = ""; +print "##fileformat=VCFv4.1\n"; +print "##INFO=\n"; +print "##INFO=\n"; +print "##FORMAT=\n"; +print "##FORMAT=\n"; +print "##FORMAT=\n"; +print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample\n"; + +while (<$fh>) { + chomp; + my @row = split(/\t/, $_); + + my %var = map { $_ , $row[$nt{$_}] } split(/\//, $row[5]); + my $varNT = (sort { $var{$b} <=> $var{$a} } keys(%var))[0]; + + my $depth = $row[$depthCol]; + my $freq = $var{$varNT} / $depth; + if (($row[2] ne ".") && ($minDepth <= $depth)) { + my $qual = 100; + my $filt = "."; + $row[2] =~ s/\|/,/g; + my $info = "TARGET:$row[2];DP:$depth"; + + if ($row[13] ne ".") { + my %ins = split(/[\|:]/, $row[13]); + my $maxIns = (sort {$ins{$b} <=> $ins{$a}} keys(%ins))[0]; + my $iFreq = $ins{$maxIns}; + my $VAF = $iFreq / ($iFreq + $row[6]); + $maxIns =~ s/^\+//; + if ($VAF > $minFreq && $minVar <= $iFreq) { + my $format = "DP:AD:VAF\tDP=$depth:AD=$row[6],$iFreq:VAF=$VAF"; + print join("\t", @row[0 .. 1], ".", $prevNT . $row[4], $prevNT . $row[4] . $maxIns, $qual, $filt, $info, $format) . "\n"; + } + } + + if ($row[14] ne ".") { + my %del = split(/[\|:]/, $row[14]); + my $maxDel = (sort {$del{$b} <=> $del{$a}} keys(%del))[0]; + my $dFreq = $del{$maxDel}; + my $VAF = $dFreq / ($dFreq + $row[6]); + $maxDel =~ s/^-//; + if ($VAF > $minFreq && $minVar <= $dFreq) { + my $format = "DP:AD:VAF\tDP=$depth:AD=$row[6],$dFreq:VAF=$VAF"; + print join("\t", @row[0 .. 1], ".", $prevNT . $maxDel, $prevNT, $qual, $filt, $info, $format) . "\n"; + } + } + + + if ($minFreq <= $freq && $minVar <= $var{$varNT}) { + my $format = "DP:AD:VAF\tDP=$depth:AD=$row[6],$var{$varNT}:VAF=$freq"; + my $varNT = substr($row[5], 0, 1); + print join("\t", @row[0 .. 1], ".", $row[4], $varNT, $qual, $filt, $info, $format) . "\n"; + } + } + $prevNT = $row[4]; +} diff -r 1b81dd6b68b5 -r 9285f791716d falco/misc/vcf2tsv.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/vcf2tsv.pl Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,73 @@ +#!/usr/bin/perl -w + +use strict; + +my @vcfs = @ARGV; + +my @info = (); +my @format = (); +my $header = ""; + +foreach my $vcf (0 .. $#vcfs) { + open V, "<$vcfs[$vcf]"; + while () { + if (/^#CHROM/) { + if ($vcf == 0) { + chomp; + my @row = split(/\t/, $_); + print $header; + print join("\t", @row[0 .. 6], @info) . "\t"; + my @sampleRow = (); + foreach my $s (9 .. $#row) { +# print join("\t", map { "S$s" . "_$_" } @format) . "\n"; + push @sampleRow, map { $row[$s] . "_$_" } @format; + } + print join("\t", @sampleRow) . "\n"; + } + last; + } + if (/^##INFO/ && ($vcf == 0)) { + /ID=(.*?),/; + push @info, $1; + } + elsif (/^##FORMAT/ && ($vcf == 0)) { + /ID=(.*?),/; + push @format, $1; + } + $header .= $_; + } + + while () { + print join("\t", @{ &readTags(\$_) }) . "\n"; + } + close V; +} + +sub readTags { + my $line = shift; + chomp $$line; + my @row = split(/\t/, $$line); + my @res = (@row[0 .. 6]); + my @infoDat = split(/[;]/, $row[7]); + my @formatDat1 = split(/:/, $row[8]); + my %infoHsh = (); + foreach my $i (@infoDat) { + my @e = split(/=/, $i); + $infoHsh{$e[0]} = defined($e[1])?$e[1]:"1"; + } + + foreach my $t (0 .. $#info) { + push @res, defined($infoHsh{$info[$t]})?$infoHsh{$info[$t]}:"."; + } + + foreach my $s (9 .. $#row) { + my %formatHsh = (); + my @formatDat2 = split(/:/, $row[$s]); + $formatHsh{$formatDat1[$_]} = $formatDat2[$_] foreach (0 .. $#formatDat1); + + foreach my $i (0 .. $#format) { + push @res, defined($formatHsh{$format[$i]})?$formatHsh{$format[$i]}:"."; + } + } + return \@res; +} diff -r 1b81dd6b68b5 -r 9285f791716d tool-data/GALAXY_EGFR.bed~ diff -r 1b81dd6b68b5 -r 9285f791716d tool-data/GALAXY_TSACP.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/GALAXY_TSACP.bed Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,221 @@ +chr1 43814981 43815163 MPL1_2.chr1.43815008.43815009_tile_1 100 + 43815005 43815137 +chr1 115256499 115256680 NRAS1_7.chr1.115256528.115256531_tile_1 100 + 115256525 115256653 +chr1 115258701 115258884 NRAS8_13.chr1.115258730.115258748_tile_1 100 + 115258727 115258855 +chr2 29432635 29432822 ALK1.chr2.29432664.29432664_tile_1 100 + 29432662 29432795 +chr2 29443666 29443836 ALK2.chr2.29443695.29443695_tile_1 100 + 29443691 29443810 +chr2 209113083 209113264 IDH1_1_2.chr2.209113112.209113113_tile_1 100 + 209113110 209113237 +chr2 212288911 212289100 ERBB4_1_2.chr2.212288942.212288955_tile_1 100 + 212288938 212289073 +chr2 212530035 212530210 ERBB4_3_4.chr2.212530066.212530135_tile_1 100 + 212530061 212530183 +chr2 212576820 212576990 ERBB4_5.chr2.212576857.212576857_tile_1 100 + 212576850 212576960 +chr2 212578314 212578499 ERBB4_6_7.chr2.212578341.212578349_tile_1 100 + 212578339 212578470 +chr2 212587114 212587285 ERBB4_8.chr2.212587147.212587147_tile_1 100 + 212587141 212587258 +chr2 212589782 212589957 ERBB4_9.chr2.212589811.212589811_tile_1 100 + 212589809 212589930 +chr2 212652705 212652876 ERBB4_10.chr2.212652764.212652764_tile_1 100 + 212652735 212652849 +chr2 212812126 212812311 ERBB4_11.chr2.212812157.212812157_tile_1 100 + 212812155 212812284 +chr3 10183768 10183952 VHL1_2.chr3.10183797.10183817_tile_1 100 + 10183793 10183926 +chr3 10188216 10188401 VHL3_5.chr3.10188245.10188301_tile_1 100 + 10188243 10188374 +chr3 10191449 10191634 VHL6_8.chr3.10191480.10191506_tile_1 100 + 10191477 10191607 +chr3 37067211 37067394 MLH1.chr3.37067240.37067240_tile_1 100 + 37067237 37067367 +chr3 41266009 41266180 CTNNB1_1_16.chr3.41266040.41266137_tile_1 100 + 41266036 41266153 +chr3 178916835 178917024 PIK3CA1.chr3.178916876.178916876_tile_1 100 + 178916861 178916997 +chr3 178921524 178921709 PIK3CA2.chr3.178921553.178921553_tile_1 100 + 178921551 178921682 +chr3 178927905 178928082 PIK3CA3.chr3.178927980.178927980_tile_1 100 + 178927932 178928055 +chr3 178936043 178936214 PIK3CA4_11.chr3.178936074.178936095_tile_1 100 + 178936070 178936187 +chr3 178938831 178939004 PIK3CA12.chr3.178938860.178938860_tile_1 100 + 178938858 178938977 +chr3 178951880 178952054 PIK3CA13_20.chr3.178952007.178952150_tile_1 100 + 178951906 178952026 +chr3 178951998 178952184 PIK3CA13_20.chr3.178952007.178952150_tile_2 100 - 178952025 178952154 +chr4 1803537 1803712 FGFR3_1_2.chr4.1803564.1803568_tile_1 100 + 1803562 1803685 +chr4 1806090 1806277 FGFR3_3_4.chr4.1806119.1806153_tile_1 100 + 1806117 1806250 +chr4 1807835 1808025 FGFR3_5_7.chr4.1807862.1807890_tile_1 100 + 1807857 1807999 +chr4 1808294 1808464 FGFR3_8.chr4.1808331.1808331_tile_1 100 + 1808316 1808442 +chr4 1808920 1809105 FGFR3_9.chr4.1808949.1808949_tile_1 100 + 1808943 1809078 +chr4 55140980 55141157 PDGFRA1_4.chr4.55141013.55141049_tile_1 100 + 55141007 55141130 +chr4 55144119 55144306 PDGFRA5.chr4.55144146.55144146_tile_1 100 + 55144145 55144279 +chr4 55144518 55144703 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36031895 +chr20 57484389 57484560 GNAS1.chr20.57484420.57484421_tile_1 100 + 57484416 57484533 +chr22 24133938 24134126 SMARCB1_1.chr22.24133967.24133990_tile_1 100 + 24133964 24134100 +chr22 24143209 24143383 SMARCB1_3.chr22.24143240.24143240_tile_1 100 + 24143235 24143357 +chr22 24145551 24145726 SMARCB1_4.chr22.24145582.24145582_tile_1 100 + 24145577 24145699 +chr22 24176323 24176495 SMARCB1_5_6.chr22.24176352.24176357_tile_1 100 + 24176350 24176469 +chr19 3114823 3115004 GNA11_4.chr19.3114942.3115070_tile_1 100 - 3114845 3114981 +chr19 3114957 3115133 GNA11_4.chr19.3114942.3115070_tile_2 100 + 3114980 3115111 +chr19 3118801 3118989 GNA11_5.chr19.3118922.3119051_tile_1 100 - 3118825 3118963 +chr19 3119207 3119395 GNA11_6.chr19.3119204.3119357_tile_2 100 - 3119232 3119373 +chr19 3120864 3121035 GNA11_7.chr19.3120987.3121177_tile_1 100 + 3120887 3121008 +chr19 3120984 3121170 GNA11_7.chr19.3120987.3121177_tile_2 100 - 3121006 3121144 +chr19 3121120 3121304 GNA11_7.chr19.3120987.3121177_tile_3 100 + 3121143 3121280 +chr9 80412405 80412592 GNAQ_4.chr9.80412436.80412564_tile_1 100 + 80412432 80412565 +chr9 80409248 80409421 GNAQ_5.chr9.80409379.80409508_tile_1 100 + 80409278 80409392 +chr9 80409334 80409510 GNAQ_5.chr9.80409379.80409508_tile_2 100 - 80409364 80409486 +chr9 80409458 80409639 GNAQ_5.chr9.80409379.80409508_tile_3 100 + 80409485 80409612 +chr9 80343305 80343476 GNAQ_6.chr9.80343430.80343583_tile_1 100 + 80343330 80343447 +chr9 80343391 80343561 GNAQ_6.chr9.80343430.80343583_tile_2 100 - 80343417 80343531 +chr9 80343503 80343689 GNAQ_6.chr9.80343430.80343583_tile_3 100 + 80343530 80343659 +chr9 80336109 80336280 GNAQ_7.chr9.80336240.80336429_tile_1 100 + 80336139 80336255 +chr9 80336203 80336374 GNAQ_7.chr9.80336240.80336429_tile_2 100 - 80336228 80336347 +chr9 80336319 80336495 GNAQ_7.chr9.80336240.80336429_tile_3 100 + 80336346 80336467 +chr22 17052963 17053133 PIK3CA4_11.chr3.178936074.178936095_tile_1 100 + 17052990 17053106 +chr22 17055412 17055585 PIK3CA12.chr3.178938860.178938860_tile_1 100 + 17055439 17055558 +chr9 33675956 33676480 PTEN7.chr10.89717615.89717772_tile_1 100 - 33675986 33676451 +chr9 33675628 33675815 PTEN13.chr10.89720716.89720852_tile_1 100 - 33675655 33675790 +chr7 65970149 65970483 GNA11_6.chr19.3119204.3119357_tile_2 100 + 65970175 65970458 +chr7 65970284 65970719 GNA11_7.chr19.3120987.3121177_tile_1 100 - 65970311 65970696 +chr2 132181237 132181750 GNAQ_5.chr9.80409379.80409508_tile_1 100 + 132181267 132181721 +chr2 132181447 132181600 GNAQ_6.chr9.80343430.80343583_tile_1 100 + 132181474 132181571 +chr2 132181331 132181839 GNAQ_7.chr9.80336240.80336429_tile_2 100 - 132181356 132181815 diff -r 1b81dd6b68b5 -r 9285f791716d tool-data/GALAXY_TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/GALAXY_TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,445 @@ +[Header] +Customer Name "ILLUMINA, INC." +Product Type 15032433 +Date Manufactured +Lot +DesignStudio ID NA +Target Plexity 212 + +[Probes] +Target Region Name Target Region ID Target ID Species Build ID Chromosome Start Position End Position Submitted Target Region Strand ULSO Sequence ULSO Genomic Hits DLSO Sequence DLSO Genomic Hits Probe Strand Designer Design Score Expected Amplifed Region Size SNP Masking Labels +MPL1_2 MPL1_2.chr1.43815008.43815009 MPL1_2.chr1.43815008.43815009_tile_1 Homo sapiens hg19 chr1 43815008 43815009 - AAGTGGCGAAGCCGTAGGTGCGCACG 0 TCAGCAGCAGCAGGCCCAGGACGG 0 - ILLUMINA NA 183 TRUE +NRAS1_7 NRAS1_7.chr1.115256528.115256531 NRAS1_7.chr1.115256528.115256531_tile_1 Homo sapiens hg19 chr1 115256528 115256531 - CAATAGCATTGCATTCCCTGTGGTTTT 0 AGAGTACAGTGCCATGAGAGACCAAT 0 - ILLUMINA NA 182 TRUE +NRAS8_13 NRAS8_13.chr1.115258730.115258748 NRAS8_13.chr1.115258730.115258748_tile_1 Homo sapiens hg19 chr1 115258730 115258748 - GGGTTTTCATTTCCATTGATTATAGAAAG 0 CTGACAATCCAGCTAATCCAGAACCA 0 - ILLUMINA NA 184 TRUE +ALK1 ALK1.chr2.29432664.29432664 ALK1.chr2.29432664.29432664_tile_1 Homo sapiens hg19 chr2 29432664 29432664 - GATAAAATCCTAGTGATGGCCGTTGTA 0 GACATCTACAGGTGAGTAAAGACTGCC 0 - ILLUMINA NA 188 TRUE +ALK2 ALK2.chr2.29443695.29443695 ALK2.chr2.29443695.29443695_tile_1 Homo sapiens hg19 chr2 29443695 29443695 - TGCTGCCCATGTTTACAGAATGCCTT 0 CACCAGAACATTGTTCGCTGCATTG 0 - ILLUMINA NA 171 TRUE +IDH1_1_2 IDH1_1_2.chr2.209113112.209113113 IDH1_1_2.chr2.209113112.209113113_tile_1 Homo sapiens hg19 chr2 209113112 209113113 - GAGGGTTGAGGAGTTCAAGTTGAAACA 0 CATGCTTATGGGGATCAAGTAAGTCAT 0 - ILLUMINA NA 182 TRUE +ERBB4_1_2 ERBB4_1_2.chr2.212288942.212288955 ERBB4_1_2.chr2.212288942.212288955_tile_1 Homo sapiens hg19 chr2 212288942 212288955 - ACTACTGGTATAGTGCTGGTTTGTTCA 0 AGAACGTTTGCCTCAGCCTCCCATCTG 0 - ILLUMINA NA 190 TRUE +ERBB4_3_4 ERBB4_3_4.chr2.212530066.212530135 ERBB4_3_4.chr2.212530066.212530135_tile_1 Homo sapiens hg19 chr2 212530066 212530135 - CATTTCAGGGTCCTGACAACTGTACAA 0 AACTGCACCCAAGGGTAAGCATTCTT 0 - ILLUMINA NA 176 TRUE +ERBB4_5 ERBB4_5.chr2.212576857.212576857 ERBB4_5.chr2.212576857.212576857_tile_1 Homo sapiens hg19 chr2 212576857 212576857 - ATACTCTGCTATTTTATAATGAAGATGCAA 0 CCAGTAACATTGACAAATTCATAAACTGTA 0 - ILLUMINA NA 171 TRUE +ERBB4_6_7 ERBB4_6_7.chr2.212578341.212578349 ERBB4_6_7.chr2.212578341.212578349_tile_1 Homo sapiens hg19 chr2 212578341 212578349 - AGGGTAAGATACATAAACACTATCAATGA 0 TGCCTGCCCTAGTTCCAAGATGGAA 0 - ILLUMINA NA 186 TRUE +ERBB4_8 ERBB4_8.chr2.212587147.212587147 ERBB4_8.chr2.212587147.212587147_tile_1 Homo sapiens hg19 chr2 212587147 212587147 - TGAAAGTAATATTTGCTGTGTTGCAGG 0 CATTCTGTGTCAAGAAATGTCCACGTA 0 - ILLUMINA NA 172 TRUE +ERBB4_9 ERBB4_9.chr2.212589811.212589811 ERBB4_9.chr2.212589811.212589811_tile_1 Homo sapiens hg19 chr2 212589811 212589811 - GCAGACTTTGATCATGGTCCTATCTCT 0 GACTGCTTTGTATGTCTGTGATTTCTC 0 - ILLUMINA NA 176 TRUE +ERBB4_10 ERBB4_10.chr2.212652764.212652764 ERBB4_10.chr2.212652764.212652764_tile_1 Homo sapiens hg19 chr2 212652764 212652764 - AATGGTGGAGTCTATGTAGACCAGAAC 0 TCTTTTTAATTTCTCAAAATGTTCTACCCT 0 - ILLUMINA NA 172 TRUE +ERBB4_11 ERBB4_11.chr2.212812157.212812157 ERBB4_11.chr2.212812157.212812157_tile_1 Homo sapiens hg19 chr2 212812157 212812157 - GTGGCTCTTAATCAGTTTCGTTACCTG 0 GGTAAGGAATATATCCAAAATGGCAAATA 0 - ILLUMINA NA 186 TRUE +VHL1_2 VHL1_2.chr3.10183797.10183817 VHL1_2.chr3.10183797.10183817_tile_1 Homo sapiens hg19 chr3 10183797 10183817 - AAAATGGACCCCGGGGCGGTAGAGGG 0 ATACGGGCAGCACGACGCGCGGACT 0 - ILLUMINA NA 185 TRUE +VHL3_5 VHL3_5.chr3.10188245.10188301 VHL3_5.chr3.10188245.10188301_tile_1 Homo sapiens hg19 chr3 10188245 10188301 - GAACTGGGCTTAATTTTTCAAGTGGTC 0 AGAAGCCCATCGTGTGTCCCTGCATCT 0 - ILLUMINA NA 186 TRUE +VHL6_8 VHL6_8.chr3.10191480.10191506 VHL6_8.chr3.10191480.10191506_tile_1 Homo sapiens hg19 chr3 10191480 10191506 - TTGATGTGCAATGCGCTCCTGTGTCAG 0 GTATACACTGGAAGGGCAAAAACCAAAT 0 - ILLUMINA NA 186 TRUE +MLH1 MLH1.chr3.37067240.37067240 MLH1.chr3.37067240.37067240_tile_1 Homo sapiens hg19 chr3 37067240 37067240 - TGGGAGTTCAAGCATCTCCTCATCTTG 0 ATCTGGTGGGCATAGACCTTATCACT 0 - ILLUMINA NA 184 TRUE +CTNNB1_1_16 CTNNB1_1_16.chr3.41266040.41266137 CTNNB1_1_16.chr3.41266040.41266137_tile_1 Homo sapiens hg19 chr3 41266040 41266137 - GGTATCCACATCCTCTTCCTCAGGATT 0 GTCCAACTCCATCAAATCAGCTATAAA 0 - ILLUMINA NA 172 TRUE +PIK3CA1 PIK3CA1.chr3.178916876.178916876 PIK3CA1.chr3.178916876.178916876_tile_1 Homo sapiens hg19 chr3 178916876 178916876 - AGGGACAACAGTTAAGCTTTATGGTTA 0 AAAAATTCTTCCCTTTCTGCTTCTTG 0 - ILLUMINA NA 190 TRUE +PIK3CA2 PIK3CA2.chr3.178921553.178921553 PIK3CA2.chr3.178921553.178921553_tile_1 Homo sapiens hg19 chr3 178921553 178921553 - ACATTCGGAGATTTGGATGTTCTCCTA 0 TCACGTAGGTTGCACAAAGAATTTTTA 0 - ILLUMINA NA 186 TRUE +PIK3CA3 PIK3CA3.chr3.178927980.178927980 PIK3CA3.chr3.178927980.178927980_tile_1 Homo sapiens hg19 chr3 178927980 178927980 - CTTCTAATCCATGAGGTACTGGCCAAA 0 AACACATTTCAAAACACTTTTCTTCCC 0 - ILLUMINA NA 178 TRUE +PIK3CA4_11 PIK3CA4_11.chr3.178936074.178936095 PIK3CA4_11.chr3.178936074.178936095_tile_1 Homo sapiens hg19 chr3 178936074 178936095 - GGTATGGTAAAAACATGCTGAGATCAG 0 CTCGTGTAGAAATTGCTTTGAGCTGTT 0 - ILLUMINA NA 172 TRUE +PIK3CA12 PIK3CA12.chr3.178938860.178938860 PIK3CA12.chr3.178938860.178938860_tile_1 Homo sapiens hg19 chr3 178938860 178938860 - TAAACAACTCTGCCCCACTGCAGTGAA 0 CTTCAAATACATCCCACATGCACGACA 0 - ILLUMINA NA 174 TRUE +PIK3CA13_20 PIK3CA13_20.chr3.178952007.178952150 PIK3CA13_20.chr3.178952007.178952150_tile_1 Homo sapiens hg19 chr3 178952007 178952150 - CCAAAGCCTCTTGCTCAGTTTTATCTAA 0 AGCCTTGTAACACATCTCCTGAAACC 0 - ILLUMINA NA 175 TRUE +PIK3CA13_20 PIK3CA13_20.chr3.178952007.178952150 PIK3CA13_20.chr3.178952007.178952150_tile_2 Homo sapiens hg19 chr3 178952007 178952150 + CATTGCATACATTCGAAAGACCCTAGC 0 AGATAACTGAGAAAATGAAAGCTCACTCTG 0 + ILLUMINA NA 187 TRUE +FGFR3_1_2 FGFR3_1_2.chr4.1803564.1803568 FGFR3_1_2.chr4.1803564.1803568_tile_1 Homo sapiens hg19 chr4 1803564 1803568 - TTGCTGCCATTCACCTCCACGTGCTTG 0 TCTGTGGGGGCAGATGACGCTCAGG 0 - ILLUMINA NA 176 TRUE +FGFR3_3_4 FGFR3_3_4.chr4.1806119.1806153 FGFR3_3_4.chr4.1806119.1806153_tile_1 Homo sapiens hg19 chr4 1806119 1806153 - GCTCAGAACCTGGTATCTACTTTCTGT 0 TAGCTGAGGATGCCTGCATACACACTG 0 - ILLUMINA NA 188 TRUE +FGFR3_5_7 FGFR3_5_7.chr4.1807862.1807890 FGFR3_5_7.chr4.1807862.1807890_tile_1 Homo sapiens hg19 chr4 1807862 1807890 - AAACAAGGCCTCAGGCGCCATCCACT 0 GCCAGCCCGAAGTCTGCGATCT 0 - ILLUMINA NA 191 TRUE +FGFR3_8 FGFR3_8.chr4.1808331.1808331 FGFR3_8.chr4.1808331.1808331_tile_1 Homo sapiens hg19 chr4 1808331 1808331 - CCGGAGGGACCCCCACCCCTGA 0 CCCCCAGCGTGAAGATCTCCCA 0 - ILLUMINA NA 171 TRUE +FGFR3_9 FGFR3_9.chr4.1808949.1808949 FGFR3_9.chr4.1808949.1808949_tile_1 Homo sapiens hg19 chr4 1808949 1808949 - AAGCTCTGTGTAGCTGTCTCTCCATCT 0 TCGTGGGCAAACACGGAGTCGTC 0 - ILLUMINA NA 186 TRUE +PDGFRA1_4 PDGFRA1_4.chr4.55141013.55141049 PDGFRA1_4.chr4.55141013.55141049_tile_1 Homo sapiens hg19 chr4 55141013 55141049 - TACCCCATGGAACTTACCAAGCACTAG 0 CTATAAATGACCAGGACAGGTAACTGG 0 - ILLUMINA NA 178 TRUE +PDGFRA5 PDGFRA5.chr4.55144146.55144146 PDGFRA5.chr4.55144146.55144146_tile_1 Homo sapiens hg19 chr4 55144146 55144146 - GTCAGCTCCATTCAAGGGACTTCTATT 0 TACAATGTTCAAATGTGGCCCCAGGT 0 - ILLUMINA NA 188 TRUE +PDGFRA6 PDGFRA6.chr4.55144547.55144547 PDGFRA6.chr4.55144547.55144547_tile_1 Homo sapiens hg19 chr4 55144547 55144547 - AACATCTCTCTTTGCACCCACCTCCGT 0 ATGATGTAAATGGGGCCTATGGGGAC 0 - ILLUMINA NA 186 TRUE +PDGFRA7_23 PDGFRA7_23.chr4.55152040.55152109 PDGFRA7_23.chr4.55152040.55152109_tile_1 Homo sapiens hg19 chr4 55152040 55152109 - AGAGATTAAAGTGAAGGAGGATGAGCC 0 TTGCGAGCAGCCAGATCACGGTGGA 0 - ILLUMINA NA 174 TRUE +KIT1 KIT1.chr4.55561764.55561764 KIT1.chr4.55561764.55561764_tile_1 Homo sapiens hg19 chr4 55561764 55561764 - GTGTTTGTTGGTGCACGTGTATTTGC 0 CCCACGCGGACTATTAAGTCTGATTTT 0 - ILLUMINA NA 179 TRUE +KIT2 KIT2.chr4.55592185.55592186 KIT2.chr4.55592185.55592186_tile_1 Homo sapiens hg19 chr4 55592185 55592186 - CAGTATGGTGTGATGCATGTATTACCA 0 CAGAAGTCTTGCCCACATCGTTGTAA 0 - ILLUMINA NA 188 TRUE +KIT3_19 KIT3_19.chr4.55593464.55593689 KIT3_19.chr4.55593464.55593689_tile_1 Homo sapiens hg19 chr4 55593464 55593689 - GAGAGAACAAATAAATGGTTACCTGTAAA 0 GTGGAATCACAAACTTTGGCAGGA 0 - ILLUMINA NA 172 TRUE +KIT3_19 KIT3_19.chr4.55593464.55593689 KIT3_19.chr4.55593464.55593689_tile_2 Homo sapiens hg19 chr4 55593464 55593689 + CGTAGCTGGCATGATGTGCATTATTG 0 ACCCATGTATGAAGTACAGTGGAAGG 0 + ILLUMINA NA 175 TRUE +KIT3_19 KIT3_19.chr4.55593464.55593689 KIT3_19.chr4.55593464.55593689_tile_3 Homo sapiens hg19 chr4 55593464 55593689 - GTGACATGGAAAGCCCCTGTTTCATA 0 TCTGTGGGGAGAAAGGGAAAAATAGAT 0 - ILLUMINA NA 185 TRUE +KIT20_21 KIT20_21.chr4.55594221.55594258 KIT20_21.chr4.55594221.55594258_tile_1 Homo sapiens hg19 chr4 55594221 55594258 - GCAGTTTATAATCTAGCATTGCCAAAAT 0 AGTTCAGACATGAGGGCTTCCCGTTCT 0 - ILLUMINA NA 189 TRUE +KIT22 KIT22.chr4.55595519.55595519 KIT22.chr4.55595519.55595519_tile_1 Homo sapiens hg19 chr4 55595519 55595519 - ACTATTTATGTAAATCAGTCTTACCAGGA 0 TAATGACCAGGGTGGGCCCTAAAAGC 0 - ILLUMINA NA 184 TRUE +KIT23 KIT23.chr4.55597495.55597497 KIT23.chr4.55597495.55597497_tile_1 Homo sapiens hg19 chr4 55597495 55597497 - CCACATTAGCATGATATACATACTCTCT 0 CTGGGAGAGATGAAACAAGTCATGACT 0 - ILLUMINA NA 187 TRUE +KIT24_28 KIT24_28.chr4.55599320.55599348 KIT24_28.chr4.55599320.55599348_tile_1 Homo sapiens hg19 chr4 55599320 55599348 - TGTGTGATATCCCTAGACAGGATTTAC 0 GGCTAGACCAAAATCACAAATCTTTGT 0 - ILLUMINA NA 184 TRUE +KIT29 KIT29.chr4.55602694.55602694 KIT29.chr4.55602694.55602694_tile_1 Homo sapiens hg19 chr4 55602694 55602694 - GAAGCAGGACACCAATGAAACTTCAAG 0 TGCCATCCACTTCACAGGTAGTCGA 0 - ILLUMINA NA 186 TRUE +KDR1 KDR1.chr4.55946114.55946257 KDR1.chr4.55946114.55946257_tile_1 Homo sapiens hg19 chr4 55946114 55946257 - ATTCTCCAGCCTGACTCGGGGACCACACTG 0 CATTTGATTTTCATTTCGACAACAGAAAAA 0 - ILLUMINA NA 173 TRUE +KDR1 KDR1.chr4.55946114.55946257 KDR1.chr4.55946114.55946257_tile_2 Homo sapiens hg19 chr4 55946114 55946257 + ATGCTTCCTTTTAAACAGGAGGAGAGC 0 GGACTGGTAGCCGCTTGTCTGGTTTGA 0 + ILLUMINA NA 188 TRUE +KDR3 KDR3.chr4.55953807.55953807 KDR3.chr4.55953807.55953807_tile_1 Homo sapiens hg19 chr4 55953807 55953807 - CTGAAGCCATAACAACAGTCTTCTGTG 0 ATTCCATTATGACAACACAGCAGGAAT 0 - ILLUMINA NA 190 TRUE +KDR4 KDR4.chr4.55955111.55955127 KDR4.chr4.55955111.55955127_tile_1 Homo sapiens hg19 chr4 55955111 55955127 - TCCTTATTTAGCATCTCACCTCGTCAG 0 AGCCCAGTCAGAGACCCACGTTTT 0 - ILLUMINA NA 174 TRUE +KDR6 KDR6.chr4.55960989.55961023 KDR6.chr4.55960989.55961023_tile_1 Homo sapiens hg19 chr4 55960989 55961023 - TTTATAGACCAAAGGGGCACGATTCCG 0 TGTAGAAGAAGAGGAAGGTACTGGCTA 0 - ILLUMINA NA 172 TRUE +KDR8 KDR8.chr4.55962507.55962507 KDR8.chr4.55962507.55962507_tile_1 Homo sapiens hg19 chr4 55962507 55962507 - GGAAATGCATGTGGTCTGTAAACTAGG 0 AACACACAGTGAGCATCGAGCTCTCA 0 - ILLUMINA NA 178 TRUE +KDR9 KDR9.chr4.55972964.55972964 KDR9.chr4.55972964.55972964_tile_1 Homo sapiens hg19 chr4 55972964 55972964 - TACCATGGTAGGCTGCGTTGGAAGTTA 0 GACAAACCCATACCCTTGTGAAGAATG 0 - ILLUMINA NA 172 TRUE +KDR10 KDR10.chr4.55979623.55979623 KDR10.chr4.55979623.55979623_tile_1 Homo sapiens hg19 chr4 55979623 55979623 - CTGGTGTCCCTGTTTTTAGCATTAAAT 0 ACCTAAAAACCCAGTCTGGGAGTGAG 0 - ILLUMINA NA 182 TRUE +KDR11 KDR11.chr4.55980348.55980348 KDR11.chr4.55980348.55980348_tile_1 Homo sapiens hg19 chr4 55980348 55980348 - TCTGTGCAAAGTTATAGGCTTATTTGC 0 AGAACTGAACTAAATGTGGGGATTGAC 0 - ILLUMINA NA 178 TRUE +FBXW7_1 FBXW7_1.chr4.153245446.153245446 FBXW7_1.chr4.153245446.153245446_tile_1 Homo sapiens hg19 chr4 153245446 153245446 - CAGTAATTGATAGGAAGAGTATCCATACT 0 AACAAGTGGAATGGAACTCAAAGACAA 0 - ILLUMINA NA 190 TRUE +FBXW7_2 FBXW7_2.chr4.153247288.153247366 FBXW7_2.chr4.153247288.153247366_tile_1 Homo sapiens hg19 chr4 153247288 153247366 - GTTTTGTTTTGTTTTTCTGTTTCTCCCT 0 TATGATGGCAGGAGGGTTGTTAGTGGAGCA 0 - ILLUMINA NA 171 TRUE +FBXW7_5 FBXW7_5.chr4.153249384.153249384 FBXW7_5.chr4.153249384.153249384_tile_1 Homo sapiens hg19 chr4 153249384 153249384 - CATACAGGTGGAGTATGGTCATCACAA 0 AAAAGGTAAGGGAAAATCTTGTCATGG 0 - ILLUMINA NA 184 TRUE +FBXW7_7 FBXW7_7.chr4.153250883.153250883 FBXW7_7.chr4.153250883.153250883_tile_1 Homo sapiens hg19 chr4 153250883 153250883 - CTGTTCCTGTTTATGCCTTCATTTTTC 0 AGTTAGTGGTTCTGATGACAACACTT 0 - ILLUMINA NA 180 TRUE +FBXW7_8 FBXW7_8.chr4.153258983.153258983 FBXW7_8.chr4.153258983.153258983_tile_1 Homo sapiens hg19 chr4 153258983 153258983 - CTGTAATTTGGGACATCTGTTAAAACAATA 0 GACTTCATTTCATTGCTCCCTAAAGAGG 0 - ILLUMINA NA 191 TRUE +APC1 APC1.chr5.112173917.112173917 APC1.chr5.112173917.112173917_tile_1 Homo sapiens hg19 chr5 112173917 112173917 - GCAGAGCTTCTTCTAAGTGCATTTCTC 0 TGAAGAAGTTCCTGGATTTTCTGTTGC 0 - ILLUMINA NA 186 TRUE +APC2 APC2.chr5.112174631.112174631 APC2.chr5.112174631.112174631_tile_1 Homo sapiens hg19 chr5 112174631 112174631 - AATTTGTTGGTCTCTCTTCTTCTTCAT 0 TTTGTTTCTGAACCATTGGCTCCCCGT 0 - ILLUMINA NA 174 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_1 Homo sapiens hg19 chr5 112175162 112175958 + CTTGCAAAGTTTCTTCTATTAACCAAGA 0 TTCTGCTAATACCCTGCAAATAGCAGA 0 + ILLUMINA NA 176 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_2 Homo sapiens hg19 chr5 112175162 112175958 - TGCTGGATTTGGTTCTAGGGTGCT 0 CCTATTTCATCTTCAGCTGATGACAAA 0 - ILLUMINA NA 171 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_3 Homo sapiens hg19 chr5 112175162 112175958 + GAAAAGATTGGAACTAGGTCAGCTGAAG 0 AGCGAAATCTCCCTCCAAAAGTGGT 0 + ILLUMINA NA 172 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_4 Homo sapiens hg19 chr5 112175162 112175958 - CTATCAAGTGAACTGACAGAAGTACATC 0 CCTGGCTGATTCTGAAGATAAACTAGAACC 0 - ILLUMINA NA 171 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_5 Homo sapiens hg19 chr5 112175162 112175958 + CACCCAAAAGTCCACCTGAACACTAT 0 ATTATAAGCCCCAGTGATCTTCCAGAT 0 + ILLUMINA NA 174 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_6 Homo sapiens hg19 chr5 112175162 112175958 - CTCTCTCTTTTCAGCAGTAGGTGCTT 0 CACTTACCATTCCACTGCATGGTTCA 0 - ILLUMINA NA 173 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_7 Homo sapiens hg19 chr5 112175162 112175958 + CAAACCAAGCGAGAAGTACCTAAAAAT 0 AAAGTACTCCAGATGGATTTTCTTGTTC 0 + ILLUMINA NA 171 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_8 Homo sapiens hg19 chr5 112175162 112175958 - CTCTGATTCTGTTTCATTCCCATTGTCATT 0 GTGGCAAAATGTAATAAAGTATCAGCATCT 0 - ILLUMINA NA 173 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_9 Homo sapiens hg19 chr5 112175162 112175958 + ATTAAGAATAATGCCTCCAGTTCAGGA 0 AGAAGAATGTATTATTTCTGCCATGCC 0 + ILLUMINA NA 190 TRUE +CSF1R1_3 CSF1R1_3.chr5.149433644.149433646 CSF1R1_3.chr5.149433644.149433646_tile_1 Homo sapiens hg19 chr5 149433644 149433646 - TCCCACCCTCAGGACTATACCAATCT 0 AGTTCTGCTGAGGAGTTGACGACAGGG 0 - ILLUMINA NA 185 TRUE +CSF1R4 CSF1R4.chr5.149453044.149453044 CSF1R4.chr5.149453044.149453044_tile_1 Homo sapiens hg19 chr5 149453044 149453044 - TCTTGGGTGGTGGGGACTATGTACCT 0 AACTTGAGCTCTGAGCAGAACCTCATC 0 - ILLUMINA NA 175 TRUE +NPM1 NPM1.chr5.170837547.170837548 NPM1.chr5.170837547.170837548_tile_1 Homo sapiens hg19 chr5 170837547 170837548 - GGTAGGGAAAGTTCTCACTCTGCATTA 0 AAAAAGAAATGTGGTTAAGGAACCAC 0 - ILLUMINA NA 186 TRUE +EGFR1 EGFR1.chr7.55211080.55211080 EGFR1.chr7.55211080.55211080_tile_1 Homo sapiens hg19 chr7 55211080 55211080 - CATCGGAACTGCTGTCTGCATTTATGA 0 GATGATCTGCAGGTTTTCCAAAGGAAT 0 - ILLUMINA NA 188 TRUE +EGFR2 EGFR2.chr7.55221822.55221822 EGFR2.chr7.55221822.55221822_tile_1 Homo sapiens hg19 chr7 55221822 55221822 - AAGCAAGGCAAACACATCCACCCAAAG 0 AAAGCTGTATTTGCCCTCGGGGTTCA 0 - ILLUMINA NA 174 TRUE +EGFR3 EGFR3.chr7.55233043.55233043 EGFR3.chr7.55233043.55233043_tile_1 Homo sapiens hg19 chr7 55233043 55233043 - AACTTGGGAGACATTTTTGATCTCTGA 0 TGCCGGGCAGGTCTTGACGCAGT 0 - ILLUMINA NA 186 TRUE +EGFR4 EGFR4.chr7.55241677.55241708 EGFR4.chr7.55241677.55241708_tile_1 Homo sapiens hg19 chr7 55241677 55241708 - GGAAATATACAGCTTGCAAGGACTCTG 0 TCAAGATCCTCAAGAGAGCTTGGTTG 0 - ILLUMINA NA 180 TRUE +EGFR9 EGFR9.chr7.55242418.55242511 EGFR9.chr7.55242418.55242511_tile_1 Homo sapiens hg19 chr7 55242418 55242511 - ATGAGAAAAGGTGGGCCTGAGGTTCAG 0 CCTATGACAGAGAGAGAAGGAAGACGTT 0 - ILLUMINA NA 190 TRUE +EGFR44 EGFR44.chr7.55249005.55249131 EGFR44.chr7.55249005.55249131_tile_1 Homo sapiens hg19 chr7 55249005 55249131 - AGGTGAGGCAGATGCCCAGCAGGCGG 0 CGCATGAATGCGATCTTGAGTTTCAA 0 - ILLUMINA NA 175 TRUE +EGFR44 EGFR44.chr7.55249005.55249131 EGFR44.chr7.55249005.55249131_tile_2 Homo sapiens hg19 chr7 55249005 55249131 + CAGCGTGGACAACCCCCACGTGT 0 GTGTGTGCAGATCGCAAAGGTAATCA 0 + ILLUMINA NA 177 TRUE +EGFR54 EGFR54.chr7.55259514.55259524 EGFR54.chr7.55259514.55259524_tile_1 Homo sapiens hg19 chr7 55259514 55259524 - CCTCCCCTGCATGTGTTAAACAATACA 0 CCAAAATCTGTGATCTTGACATGCTGC 0 - ILLUMINA NA 178 TRUE +MET1 MET1.chr7.116339642.116339642 MET1.chr7.116339642.116339642_tile_1 Homo sapiens hg19 chr7 116339642 116339642 - CCTTCTCACTGATATCGAATGCAATGG 0 CTTCTATCTGTGGGGAGAATATGCAGT 0 - ILLUMINA NA 180 TRUE +MET2 MET2.chr7.116340262.116340262 MET2.chr7.116340262.116340262_tile_1 Homo sapiens hg19 chr7 116340262 116340262 - GCCCTGGATATTCTTTTTGAGACTGAT 0 GAAGAAGTCGTTGACATATTTGATAGG 0 - ILLUMINA NA 188 TRUE +MET3 MET3.chr7.116411990.116411990 MET3.chr7.116411990.116411990_tile_1 Homo sapiens hg19 chr7 116411990 116411990 - TGCAAAACCAAAAATAAACAACAATGTC 0 TTACACTTCGGGCACTTACAAGCCTA 0 - ILLUMINA NA 171 TRUE +MET4 MET4.chr7.116417463.116417464 MET4.chr7.116417463.116417464_tile_1 Homo sapiens hg19 chr7 116417463 116417464 - CACAAGGGGAAAGTGTAAATCAACGTTT 0 CACAACCAAAATGCCCTGTGCAAAAGA 0 - ILLUMINA NA 191 TRUE +MET6 MET6.chr7.116423413.116423474 MET6.chr7.116423413.116423474_tile_1 Homo sapiens hg19 chr7 116423413 116423474 - GAGGAGAAACTCAGAGATAACCAATAC 0 TGTCTCTGGCAAGACCAAAATCAGCA 0 - ILLUMINA NA 172 TRUE +SMO1 SMO1.chr7.128845101.128845101 SMO1.chr7.128845101.128845101_tile_1 Homo sapiens hg19 chr7 128845101 128845101 - TGACCAGGGTGAAGAGCGTGCAGAG 0 AAGGGCACTTCGCACTGGCCTGAA 0 - ILLUMINA NA 186 TRUE +SMO2 SMO2.chr7.128846040.128846040 SMO2.chr7.128846040.128846040_tile_1 Homo sapiens hg19 chr7 128846040 128846040 - ATTGCCACAGTGAGGACAAAGGGGAGT 0 GTACACGATGACAAAGATGATGACGCA 0 - ILLUMINA NA 186 TRUE +SMO3 SMO3.chr7.128846374.128846374 SMO3.chr7.128846374.128846374_tile_1 Homo sapiens hg19 chr7 128846374 128846374 - TAGCTGGGGTTTCAGCATGGGGGCAGC 0 AAGCCCGCACGGTATCGGTAGTTCT 0 - ILLUMINA NA 190 TRUE +SMO4 SMO4.chr7.128850341.128850341 SMO4.chr7.128850341.128850341_tile_1 Homo sapiens hg19 chr7 128850341 128850341 - AACCACTGACCAAGGCTGTGCTAGAGG 0 TCATGGCGATGCCAGTTCCAAACA 0 - ILLUMINA NA 190 TRUE +SMO5 SMO5.chr7.128851593.128851593 SMO5.chr7.128851593.128851593_tile_1 Homo sapiens hg19 chr7 128851593 128851593 - TTCAGATCCTCTGGGGCCTTTCCTTC 0 AGAAATATCCTGGGGCAGTATGGCTCC 0 - ILLUMINA NA 173 TRUE +BRAF1 BRAF1.chr7.140453121.140453193 BRAF1.chr7.140453121.140453193_tile_1 Homo sapiens hg19 chr7 140453121 140453193 - ACCTAAACTCTTCATAATGCTTGCTCT 0 GGTCCCATCAGTTTGAACAGTTGTCT 0 - ILLUMINA NA 176 TRUE +BRAF28 BRAF28.chr7.140481397.140481478 BRAF28.chr7.140481397.140481478_tile_1 Homo sapiens hg19 chr7 140481397 140481478 - GGTTTTCTTTTTCTGTTTGGCTTGACT 0 CTACAAGGGAAAGTGGCATGGTAAGTA 0 - ILLUMINA NA 178 TRUE +FGFR1_1 FGFR1_1.chr8.38282209.38282209 FGFR1_1.chr8.38282209.38282209_tile_1 Homo sapiens hg19 chr8 38282209 38282209 - TTTTGAGAGGCTTGGGCTCAGCAGAA 0 TCACCGGCCCATCCTGCAAGCAGGG 0 - ILLUMINA NA 179 TRUE +FGFR1_2 FGFR1_2.chr8.38285938.38285938 FGFR1_2.chr8.38285938.38285938_tile_1 Homo sapiens hg19 chr8 38285938 38285938 - AAGAGATCATCACTAAGGGAGCAGTGG 0 GGATGATGATGATGATGATGACTCCTC 0 - ILLUMINA NA 184 TRUE +JAK2_1 JAK2_1.chr9.5073769.5073770 JAK2_1.chr9.5073769.5073770_tile_1 Homo sapiens hg19 chr9 5073769 5073770 - TTCAGTTTCAAAAATACTTAACTCCTGTT 0 CTCCATAATTTAAAACCAAATGCTTGTG 0 - ILLUMINA NA 188 TRUE +CDKN2A1 CDKN2A1.chr9.21971153.21971187 CDKN2A1.chr9.21971153.21971187_tile_1 Homo sapiens hg19 chr9 21971153 21971187 - TTGTGTGGGGGTCTGCTTGGCGGTGA 0 AACTGCGCCGACCCCGCCACTCTCA 0 - ILLUMINA NA 187 TRUE +ABL1_1 ABL1_1.chr9.133738330.133738364 ABL1_1.chr9.133738330.133738364_tile_1 Homo sapiens hg19 chr9 133738330 133738364 - ATGCATCGCCTAATGCCAGCAGACGC 0 TGATGTCCGTGCGTTCCATCTCCCAC 0 - ILLUMINA NA 191 TRUE +ABL1_9 ABL1_9.chr9.133747520.133747520 ABL1_9.chr9.133747520.133747520_tile_1 Homo sapiens hg19 chr9 133747520 133747520 - AGCGCCTGTGTCACCCTGGGGGT 0 AAAACGAAGGTGAAATTATTTCAGGAA 0 - ILLUMINA NA 190 TRUE +ABL1_10 ABL1_10.chr9.133748283.133748414 ABL1_10.chr9.133748283.133748414_tile_1 Homo sapiens hg19 chr9 133748283 133748414 + AGAATCCTTCAGAAGGCTTTTTCTTTAGAC 0 AACCTCCTGGACTACCTGAGGGAGT 0 + ILLUMINA NA 172 TRUE +ABL1_10 ABL1_10.chr9.133748283.133748414 ABL1_10.chr9.133748283.133748414_tile_2 Homo sapiens hg19 chr9 133748283 133748414 - TCCATGGCGCAGGCTGCCTGGCC 0 CCGTAGGTCATGAACTCAGTGATGA 0 - ILLUMINA NA 182 TRUE +ABL1_16 ABL1_16.chr9.133750356.133750356 ABL1_16.chr9.133750356.133750356_tile_1 Homo sapiens hg19 chr9 133750356 133750356 - GGGAAGAGCAAGAAAGAGGCAGAAAAA 0 TGTGTAGGTGTCCCCTGTCATCAA 0 - ILLUMINA NA 190 TRUE +NOTCH1_1 NOTCH1_1.chr9.139397768.139397768 NOTCH1_1.chr9.139397768.139397768_tile_1 Homo sapiens hg19 chr9 139397768 139397768 - AGACCTGGCTTCCCACCACCCCAGGCT 0 AGATTGACAACCGGCAGTGTGTGCAG 0 - ILLUMINA NA 190 TRUE +NOTCH1_2 NOTCH1_2.chr9.139399344.139399422 NOTCH1_2.chr9.139399344.139399422_tile_1 Homo sapiens hg19 chr9 139399344 139399422 - AGTGCGAGTGGGACGGGCTGGACTGT 0 ACACCAACGTGGTCTTCAAGCGTGAC 0 - ILLUMINA NA 171 TRUE +RET1 RET1.chr10.43609078.43609104 RET1.chr10.43609078.43609104_tile_1 Homo sapiens hg19 chr10 43609078 43609104 - ACTCGCCTCCCAGCAATTTCCTCCC 0 TTGCAGGTGCCATAGCCAGCTTTAAT 0 - ILLUMINA NA 180 TRUE +RET2_9 RET2_9.chr10.43609940.43609950 RET2_9.chr10.43609940.43609950_tile_1 Homo sapiens hg19 chr10 43609940 43609950 + AAGCCTCACACCACCCCCACCCACAGAT 0 CCCATCTCCTCAGCTGAGATGACCTT 0 + ILLUMINA NA 175 TRUE +RET10 RET10.chr10.43613840.43613840 RET10.chr10.43613840.43613840_tile_1 Homo sapiens hg19 chr10 43613840 43613840 - AGAACAGGGCTGTATGGAGCCCCCAGC 0 GGGAGGCGTTCTCTGAAATGCAG 0 - ILLUMINA NA 190 TRUE +RET11_12 RET11_12.chr10.43615567.43615569 RET11_12.chr10.43615567.43615569_tile_1 Homo sapiens hg19 chr10 43615567 43615569 - ATGGTGCACCTGGGATCCCTGGGAG 0 ATGTTTCTGGCTGCCAAGTCCCGATGAA 0 - ILLUMINA NA 172 TRUE +RET13 RET13.chr10.43617416.43617416 RET13.chr10.43617416.43617416_tile_1 Homo sapiens hg19 chr10 43617416 43617416 - AATTCCCTGGCCAAGCTGCACAGACGG 0 CCATTTAACTGGAATCCGACCCTAAAG 0 - ILLUMINA NA 178 TRUE +PTEN1 PTEN1.chr10.89624242.89624244 PTEN1.chr10.89624242.89624244_tile_1 Homo sapiens hg19 chr10 89624242 89624244 - TACGGACATTTTCGCATCCGTCTACTC 0 ATGATGGCTGTCATGTCTGGGAGCCTG 0 - ILLUMINA NA 176 TRUE +PTEN3 PTEN3.chr10.89685307.89685307 PTEN3.chr10.89685307.89685307_tile_1 Homo sapiens hg19 chr10 89685307 89685307 - TGGACTTCTTGACTTAATCGGTTTAGG 0 CTTGTAATGGTTTTTATGCTTTGAATCCA 0 - ILLUMINA NA 186 TRUE +PTEN4 PTEN4.chr10.89711893.89711900 PTEN4.chr10.89711893.89711900_tile_1 Homo sapiens hg19 chr10 89711893 89711900 - GGATGAGAATTTCAAGCACTTACTGCA 0 TGGGAATAGTTACTCCCTGGTGGACA 0 - ILLUMINA NA 176 TRUE +PTEN7 PTEN7.chr10.89717615.89717772 PTEN7.chr10.89717615.89717772_tile_1 Homo sapiens hg19 chr10 89717615 89717772 - GGGTCCTGAATTGGAGGAATATATCTTCAC 0 ACACGAAATATGGATTCTGTATCTGC 0 - ILLUMINA NA 181 TRUE +PTEN7 PTEN7.chr10.89717615.89717772 PTEN7.chr10.89717615.89717772_tile_2 Homo sapiens hg19 chr10 89717615 89717772 + CAGTTTGTGGTCTGCCAGCTAAA 0 AAAGGTTTGTACTTTACTTTCATTGGGAG 0 + ILLUMINA NA 188 TRUE +PTEN13 PTEN13.chr10.89720716.89720852 PTEN13.chr10.89720716.89720852_tile_1 Homo sapiens hg19 chr10 89720716 89720852 - AATTTGGAGAAAAGTATCGGTTGGCTT 0 AGGTTTCCTCTGGTCCTGGTATGAA 0 - ILLUMINA NA 188 TRUE +PTEN13 PTEN13.chr10.89720716.89720852 PTEN13.chr10.89720716.89720852_tile_2 Homo sapiens hg19 chr10 89720716 89720852 + AAAATGATCTTGACAAAGCAAATAAAGAC 0 CTTGCTTGACAAGTTTTTAACTTATGTATT 0 + ILLUMINA NA 179 TRUE +FGFR2_1 FGFR2_1.chr10.123258034.123258034 FGFR2_1.chr10.123258034.123258034_tile_1 Homo sapiens hg19 chr10 123258034 123258034 - CTAACAGTAGCTGCCCATGAGTTAGAG 0 TTCTTGGAGCCTGCACACAGGATGGTG 0 - ILLUMINA NA 180 TRUE +FGFR2_2 FGFR2_2.chr10.123274774.123274803 FGFR2_2.chr10.123274774.123274803_tile_1 Homo sapiens hg19 chr10 123274774 123274803 - GCCTTTTGGTTCCTTTGGTTGTGCTAT 0 CATAGGGGTCTTCTTAATCGCCTGTAT 0 - ILLUMINA NA 186 TRUE +FGFR2_5 FGFR2_5.chr10.123279503.123279677 FGFR2_5.chr10.123279503.123279677_tile_1 Homo sapiens hg19 chr10 123279503 123279677 - CACGTGGAAAAGAACGGCAGTAAATAC 0 GGAGTTGAGAGAGGATGATTCTCTTTT 0 - ILLUMINA NA 172 TRUE +FGFR2_5 FGFR2_5.chr10.123279503.123279677 FGFR2_5.chr10.123279503.123279677_tile_2 Homo sapiens hg19 chr10 123279503 123279677 + TTTAGATTCAGAAAGTCCTCACCTTGAG 0 CTCCTCCGACCACTGTGGAGGCATTT 0 + ILLUMINA NA 171 TRUE +FGFR2_5 FGFR2_5.chr10.123279503.123279677 FGFR2_5.chr10.123279503.123279677_tile_3 Homo sapiens hg19 chr10 123279503 123279677 - ACTGACAGCCCTCTGGACAACACAGCT 0 CGTAGAGTTTGTCTGCAAGGTTTACAG 0 - ILLUMINA NA 184 TRUE +HRAS1 HRAS1.chr11.533873.533875 HRAS1.chr11.533873.533875_tile_1 Homo sapiens hg19 chr11 533873 533875 - TACCAGGGAGAGGCTGGCTGTGTGAAC 0 AGTACAGCGCCATGCGGGACCAGTAC 0 - ILLUMINA NA 180 TRUE +HRAS6 HRAS6.chr11.534285.534289 HRAS6.chr11.534285.534289_tile_1 Homo sapiens hg19 chr11 534285 534289 - CTGCCCTGTGGGGCCTGGGGCTGG 0 AAGAGTGCGCTGACCATCCAGCTGATC 0 - ILLUMINA NA 185 TRUE +ATM1 ATM1.chr11.108117847.108117848 ATM1.chr11.108117847.108117848_tile_1 Homo sapiens hg19 chr11 108117847 108117848 - GAAAGGAATAGTTGCATGTACAGAGTC 0 GATATCTGCCATCAATTCAATCAAATTTT 0 - ILLUMINA NA 174 TRUE +ATM2 ATM2.chr11.108119823.108119823 ATM2.chr11.108119823.108119823_tile_1 Homo sapiens hg19 chr11 108119823 108119823 - TTGCTAGTAATAGGTTTGGGGGTAGAC 0 GATCAAAATCATTCTGTGACTTCTGAA 0 - ILLUMINA NA 172 TRUE +ATM3 ATM3.chr11.108123551.108123551 ATM3.chr11.108123551.108123551_tile_1 Homo sapiens hg19 chr11 108123551 108123551 - AAGCTATAGCTTAAAATGATAAAGAGCAT 0 ACAAAGAAAAACAAAAAGCTTCACTTAGA 0 - ILLUMINA NA 172 TRUE +ATM4 ATM4.chr11.108137973.108138003 ATM4.chr11.108137973.108138003_tile_1 Homo sapiens hg19 chr11 108137973 108138003 - ACTGCCAAATCAATATAAAGAAGTAAAAGA 0 GATTTCCATTAGTATCATCTTCCATTGAT 0 - ILLUMINA NA 189 TRUE +ATM6 ATM6.chr11.108155132.108155132 ATM6.chr11.108155132.108155132_tile_1 Homo sapiens hg19 chr11 108155132 108155132 - TCGAATAAATAGCCTTAAAACTTAAAGGTT 0 ATCCCACTGTCTCTGGTACCCTCATAG 0 - ILLUMINA NA 179 TRUE +ATM7 ATM7.chr11.108170476.108170479 ATM7.chr11.108170476.108170479_tile_1 Homo sapiens hg19 chr11 108170476 108170479 - ACTCACCAATCTTCTACCAGTGTGTTA 0 ACTTCTCCCAAGCAGCTTCCAACAGCC 0 - ILLUMINA NA 178 TRUE +ATM9 ATM9.chr11.108172421.108172421 ATM9.chr11.108172421.108172421_tile_1 Homo sapiens hg19 chr11 108172421 108172421 - ACAGAACTGTTTTAGATATGCTGGGTA 0 AATGTTTTTCAAACAGGTAACAGCTGC 0 - ILLUMINA NA 182 TRUE +ATM10 ATM10.chr11.108173640.108173640 ATM10.chr11.108173640.108173640_tile_1 Homo sapiens hg19 chr11 108173640 108173640 - CAGGTCATAAACAAGGAATTATATCAGACT 0 ATATCATCCAGGCCTTCAAAAGGG 0 - ILLUMINA NA 191 TRUE +ATM11 ATM11.chr11.108180945.108180945 ATM11.chr11.108180945.108180945_tile_1 Homo sapiens hg19 chr11 108180945 108180945 - CCCTTATTGAGACAATGCCAACATTAA 0 CTAGATAATTTAAATCCAGCCAGAAAGC 0 - ILLUMINA NA 188 TRUE +ATM12 ATM12.chr11.108200958.108200961 ATM12.chr11.108200958.108200961_tile_1 Homo sapiens hg19 chr11 108200958 108200961 - CAAAGTCGGAATACCCACATATCATGT 0 CCTTTACTGTGTATCTTGCATAGAATAAT 0 - ILLUMINA NA 172 TRUE +ATM14 ATM14.chr11.108204681.108204681 ATM14.chr11.108204681.108204681_tile_1 Homo sapiens hg19 chr11 108204681 108204681 - TAGGTTGAAACATATGAAATTTGCCAA 0 GGGACAACAACATCTTCTAAATTCTTAAG 0 - ILLUMINA NA 174 TRUE +ATM15 ATM15.chr11.108205769.108205769 ATM15.chr11.108205769.108205769_tile_1 Homo sapiens hg19 chr11 108205769 108205769 - GACAAAATCCCAAATAAAGCAGAAAGAA 0 CCTGCTAAGCGAAATTCTGCTTTAAATG 0 - ILLUMINA NA 191 TRUE +ATM16 ATM16.chr11.108206594.108206594 ATM16.chr11.108206594.108206594_tile_1 Homo sapiens hg19 chr11 108206594 108206594 - CACCCAACCAAATGGCATCTTTTATAT 0 TTGTCTCAGGTCATCACGGCCCTTCAG 0 - ILLUMINA NA 186 TRUE +ATM17 ATM17.chr11.108218089.108218089 ATM17.chr11.108218089.108218089_tile_1 Homo sapiens hg19 chr11 108218089 108218089 - CTAGGACAACTGTTTATGCTGAAAACA 0 TCTATATGTACAAGTTCTGCTGACTGC 0 - ILLUMINA NA 188 TRUE +ATM18 ATM18.chr11.108225590.108225590 ATM18.chr11.108225590.108225590_tile_1 Homo sapiens hg19 chr11 108225590 108225590 - GCTAAGTGCACAATCTCCTCCTTTCT 0 AACAGAGTTTCCTGAGAGTTTCTCATC 0 - ILLUMINA NA 191 TRUE +ATM19 ATM19.chr11.108236086.108236203 ATM19.chr11.108236086.108236203_tile_1 Homo sapiens hg19 chr11 108236086 108236203 - TGAAGATCACACCCAAGCTTTCCATC 0 TCAGCTACTTTGTTGAAACTCTGGTCA 0 - ILLUMINA NA 185 TRUE +KRAS1 KRAS1.chr12.25378562.25378562 KRAS1.chr12.25378562.25378562_tile_1 Homo sapiens hg19 chr12 25378562 25378562 - TCTTTCCCAGAGAACAAATTAAAAGAGT 0 AGACAAGACAGGTAAGTAACACTGAAA 0 - ILLUMINA NA 187 TRUE +KRAS2 KRAS2.chr12.25380275.25380283 KRAS2.chr12.25380275.25380283_tile_1 Homo sapiens hg19 chr12 25380275 25380283 - TTGTTGTTGAGTTGTATATAACACCTTTT 0 AGTACAGTGCAATGAGGGACCAGTAC 0 - ILLUMINA NA 184 TRUE +KRAS7 KRAS7.chr12.25398255.25398285 KRAS7.chr12.25398255.25398285_tile_1 Homo sapiens hg19 chr12 25398255 25398285 - GGTACTGGTGGAGTATTTGATAGTGTAT 0 GCTAATTCAGAATCATTTTGTGGACGAAT 0 - ILLUMINA NA 191 TRUE +PTPN11_1 PTPN11_1.chr12.112888163.112888211 PTPN11_1.chr12.112888163.112888211_tile_1 Homo sapiens hg19 chr12 112888163 112888211 - TACTGACCTTTCAGAGGTAGGATCTGC 0 GTGTTCTGAATCTTGATGTGGGTGAC 0 - ILLUMINA NA 190 TRUE +PTPN11_10 PTPN11_10.chr12.112926884.112926888 PTPN11_10.chr12.112926884.112926888_tile_1 Homo sapiens hg19 chr12 112926884 112926888 - CAAGAGGCCTAGCAAGAGAATGAGAAT 0 TCTGAGACCGCACCATCTGGATGGTT 0 - ILLUMINA NA 178 TRUE +HNF1A_1 HNF1A_1.chr12.121431413.121431414 HNF1A_1.chr12.121431413.121431414_tile_1 Homo sapiens hg19 chr12 121431413 121431414 - TTGCCGCAGCCCAGACCAAACCAGCA 0 TTGAAACGGTTCCTCCGCCCCTTCTT 0 - ILLUMINA NA 175 TRUE +HNF1A_3 HNF1A_3.chr12.121432070.121432070 HNF1A_3.chr12.121432070.121432070_tile_1 Homo sapiens hg19 chr12 121432070 121432070 - ACATACCACTTACCGTGGACCTTACT 0 CGGTTGGCAAACCAGTTGTAGACA 0 - ILLUMINA NA 181 TRUE +FLT3_1 FLT3_1.chr13.28592620.28592653 FLT3_1.chr13.28592620.28592653_tile_1 Homo sapiens hg19 chr13 28592620 28592653 - CACATCACAGTAAATAACACTCTGGTG 0 TTGTCAGGGGCAATGTGAGGCTGCTATT 0 - ILLUMINA NA 178 TRUE +FLT3_13 FLT3_13.chr13.28602329.28602329 FLT3_13.chr13.28602329.28602329_tile_1 Homo sapiens hg19 chr13 28602329 28602329 - ACTTGAGTTTTACATTTTTAATGCTCCT 0 TGTCAGGTAACCCACTTCCACGAAAA 0 - ILLUMINA NA 171 TRUE +FLT3_14 FLT3_14.chr13.28608244.28608341 FLT3_14.chr13.28608244.28608341_tile_1 Homo sapiens hg19 chr13 28608244 28608341 - CTATCTGCAGAACTGCCTATTCCTAAC 0 TTCCAAGAGAAAATTTAGAGTTTGGTAAG 0 - ILLUMINA NA 190 TRUE +FLT3_22 FLT3_22.chr13.28610138.28610138 FLT3_22.chr13.28610138.28610138_tile_1 Homo sapiens hg19 chr13 28610138 28610138 + CCAGGTCCAAGATGGTAATGGGTAT 0 ATACCAATACTTTGTGAAGCCAAGGTGG 0 + ILLUMINA NA 171 TRUE +RB1_1 RB1_1.chr13.48919244.48919244 RB1_1.chr13.48919244.48919244_tile_1 Homo sapiens hg19 chr13 48919244 48919244 - CCTTTCCAATTTGCTGAAGAGTGCAAA 0 CAGTAACCTTAAAAATTTGTGTTATTTCGT 0 - ILLUMINA NA 182 TRUE +RB1_2 RB1_2.chr13.48923148.48923148 RB1_2.chr13.48923148.48923148_tile_1 Homo sapiens hg19 chr13 48923148 48923148 - GCTAACAGTTAATAAGCCAAGCAGAGA 0 AAATGTGATCCAAGAAACTTTTAGCAC 0 - ILLUMINA NA 178 TRUE +RB1_3 RB1_3.chr13.48942685.48942685 RB1_3.chr13.48942685.48942685_tile_1 Homo sapiens hg19 chr13 48942685 48942685 - ACATAAAGAAACGTGAACAAATCTGAAA 0 GGTGTTCTCTGTGTTTCAAAACTAAATAA 0 - ILLUMINA NA 173 TRUE +RB1_4 RB1_4.chr13.48955538.48955550 RB1_4.chr13.48955538.48955550_tile_1 Homo sapiens hg19 chr13 48955538 48955550 - TTCCCTATATGTTCTTGAGGTAGATGT 0 AATGTTTTATCATTTCTCTTGTCAAGTTG 0 - ILLUMINA NA 182 TRUE +RB1_6 RB1_6.chr13.49027168.49027168 RB1_6.chr13.49027168.49027168_tile_1 Homo sapiens hg19 chr13 49027168 49027168 - TTTGCAGTTTGAATGGTCAACATAACA 0 TAAAGGTGAATCCTATATGAAACATGATG 0 - ILLUMINA NA 178 TRUE +RB1_7 RB1_7.chr13.49033843.49033846 RB1_7.chr13.49033843.49033846_tile_1 Homo sapiens hg19 chr13 49033843 49033846 - GAAGTGCTTGATTTTCTTACTTGGTCC 0 TAGGCTAGCCGATACACTGTGGGAATA 0 - ILLUMINA NA 178 TRUE +RB1_8 RB1_8.chr13.49037877.49037877 RB1_8.chr13.49037877.49037877_tile_1 Homo sapiens hg19 chr13 49037877 49037877 - GGAAAATTACCTACCTCCTGAACAGCA 0 AGTAGTCAGAATTTTATTACATGGTTTTGT 0 - ILLUMINA NA 172 TRUE +RB1_9 RB1_9.chr13.49039164.49039164 RB1_9.chr13.49039164.49039164_tile_1 Homo sapiens hg19 chr13 49039164 49039164 - TGTTTTGGTGGACCCATTACATTAGAT 0 CTTTGATCAAAACACGTTTGAATGTCT 0 - ILLUMINA NA 174 TRUE +AKT1 AKT1.chr14.105246455.105246455 AKT1.chr14.105246455.105246455_tile_1 Homo sapiens hg19 chr14 105246455 105246455 - TCTGACGGGTAGAGTGTGCGTGGCTC 0 GCTCCCCTCAACAACTTCTCTGTG 0 - ILLUMINA NA 173 TRUE +CDH1_1 CDH1_1.chr16.68835649.68835650 CDH1_1.chr16.68835649.68835650_tile_1 Homo sapiens hg19 chr16 68835649 68835650 - GGCGGTGGTGGTGCCCCACTGT 0 CTTTGAATCGGGTGTCGAGGGAAAAA 0 - ILLUMINA NA 171 TRUE +CDH1_2 CDH1_2.chr16.68846137.68846137 CDH1_2.chr16.68846137.68846137_tile_1 Homo sapiens hg19 chr16 68846137 68846137 - ACATTCTCTAGTCTGGAGAGAGTTTTC 0 TTGGTGTCAGTGACTGTGATCACAGCT 0 - ILLUMINA NA 176 TRUE +CDH1_3 CDH1_3.chr16.68847274.68847277 CDH1_3.chr16.68847274.68847277_tile_1 Homo sapiens hg19 chr16 68847274 68847277 - CATCTTGCCAGGTACCATACAAACCTT 0 CACTTTCAGTGTGGTGATTACGACGTT 0 - ILLUMINA NA 178 TRUE +TP53_1 TP53_1.chr17.7574003.7574021 TP53_1.chr17.7574003.7574021_tile_1 Homo sapiens hg19 chr17 7574003 7574021 - ACTAAATGCATGTTGCTTTTGTACCGT 0 AGAGCTGAATGAGGCCTTGGAACTC 0 - ILLUMINA NA 172 TRUE +TP53_3 TP53_3.chr17.7577022.7577129 TP53_3.chr17.7577022.7577129_tile_1 Homo sapiens hg19 chr17 7577022 7577129 - ATCCTGAGTAGTGGTAATCTACTGGGA 0 AGGTAAGCAAGCAGGACAAGAAGCG 0 - ILLUMINA NA 172 TRUE +TP53_17 TP53_17.chr17.7577523.7577574 TP53_17.chr17.7577523.7577574_tile_1 Homo sapiens hg19 chr17 7577523 7577574 - AAAAAGGCCTCCCCTGCTTGCCACAGG 0 ATCATCACACTGGAAGACTCCAGGTCA 0 - ILLUMINA NA 190 TRUE +TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_1 Homo sapiens hg19 chr17 7578190 7578536 - TTTGGATGACAGAAACACTTTTCGACA 0 CCTGCTGCTTATTTGACCTCCCTATAAC 0 - ILLUMINA NA 172 TRUE +TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_2 Homo sapiens hg19 chr17 7578190 7578536 + GACCCCAGTTGCAAACCAGACCTCA 0 TGAGGAATCAGAGGCCTGGGGA 0 + ILLUMINA NA 171 TRUE +TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_3 Homo sapiens hg19 chr17 7578190 7578536 - TTGTGAGGCGCTGCCCCCACCATGAG 0 GCATCTTATCCGAGTGGAAGGAAATTTG 0 - ILLUMINA NA 171 TRUE +TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_4 Homo sapiens hg19 chr17 7578190 7578536 + CGTCTCTCCAGCCCCAGCTGCTCACCAT 0 CCACAGCTGCACAGGGCAGGTCTT 0 + ILLUMINA NA 171 TRUE +TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_5 Homo sapiens hg19 chr17 7578190 7578536 - GCATGTTTGTTTCTTTGCTGCCGTCT 0 TTGATTCCACACCCCCGCCCGGC 0 - ILLUMINA NA 179 TRUE +TP53_60 TP53_60.chr17.7579358.7579403 TP53_60.chr17.7579358.7579403_tile_1 Homo sapiens hg19 chr17 7579358 7579403 - AGATGAAGCTCCCAGAATGCCAGAGG 0 TTCTTGCATTCTGGGACAGCCAAGTCT 0 - ILLUMINA NA 185 TRUE +TP53_64 TP53_64.chr17.7579882.7579882 TP53_64.chr17.7579882.7579882_tile_1 Homo sapiens hg19 chr17 7579882 7579882 - ATGGTGTTGGGGGAGGGGGTTCCTTCT 0 CCCCTCTGAGTCAGGAAACATTTTCAG 0 - ILLUMINA NA 182 TRUE +ERBB2_1 ERBB2_1.chr17.37880219.37880261 ERBB2_1.chr17.37880219.37880261_tile_1 Homo sapiens hg19 chr17 37880219 37880261 - CATATCTCCCCAAACCCCAATGAAGAG 0 CTTTGATGGCCACTGGAATTTTCACA 0 - ILLUMINA NA 172 TRUE +ERBB2_4 ERBB2_4.chr17.37880993.37881012 ERBB2_4.chr17.37880993.37881012_tile_1 Homo sapiens hg19 chr17 37880993 37881012 - ATACACCAGTTCAGCAGGTCCTGGGAG 0 TATGCTTCCTGGGGACAAGGGTAC 0 - ILLUMINA NA 190 TRUE +ERBB2_13 ERBB2_13.chr17.37881332.37881440 ERBB2_13.chr17.37881332.37881440_tile_1 Homo sapiens hg19 chr17 37881332 37881440 - TCTGCTCCTTGGTCCTTCACCTAACCT 0 ACATCCTCCAGGTAGCTCATCCCCTGG 0 - ILLUMINA NA 186 TRUE +SMAD4_1 SMAD4_1.chr18.48575169.48575170 SMAD4_1.chr18.48575169.48575170_tile_1 Homo sapiens hg19 chr18 48575169 48575170 - TACAAAAATTGAAACACTATTGAGATCCT 0 CGCATACTGACAATATTTAACATGTTTTAG 0 - ILLUMINA NA 172 TRUE +SMAD4_2 SMAD4_2.chr18.48581198.48581198 SMAD4_2.chr18.48581198.48581198_tile_1 Homo sapiens hg19 chr18 48581198 48581198 - ATGTTGGGAAAGTTGGCAGTGCTGGTA 0 CAAAGTCATGCACATATTCATCCTTCAC 0 - ILLUMINA NA 180 TRUE +SMAD4_3 SMAD4_3.chr18.48584560.48584560 SMAD4_3.chr18.48584560.48584560_tile_1 Homo sapiens hg19 chr18 48584560 48584560 - GCTGTCTAAAAATTAAGGCCCACATGG 0 TGATGCTATCTGCAACAGTCCTTCAC 0 - ILLUMINA NA 188 TRUE +SMAD4_4 SMAD4_4.chr18.48586262.48586262 SMAD4_4.chr18.48586262.48586262_tile_1 Homo sapiens hg19 chr18 48586262 48586262 - ACTCATGTCATGATGAGTATTGTACTC 0 AATGCAAGCTCATTGTGAACAGGCCCT 0 - ILLUMINA NA 184 TRUE +SMAD4_5 SMAD4_5.chr18.48591826.48591919 SMAD4_5.chr18.48591826.48591919_tile_1 Homo sapiens hg19 chr18 48591826 48591919 - CAATACCTTGCTCTCTCAATGGCTTCT 0 AGTAAGCAATGGAACACCAATACTCAG 0 - ILLUMINA NA 188 TRUE +SMAD4_11 SMAD4_11.chr18.48593405.48593405 SMAD4_11.chr18.48593405.48593405_tile_1 Homo sapiens hg19 chr18 48593405 48593405 - GCACTTGGGTAGATCTTATGAACAGCA 0 TGCCTATGTGCAACCTTAGGAAGAAA 0 - ILLUMINA NA 172 TRUE +SMAD4_12 SMAD4_12.chr18.48603032.48603094 SMAD4_12.chr18.48603032.48603094_tile_1 Homo sapiens hg19 chr18 48603032 48603094 - AAAGAATGAAAAGCATACTTACTGATAGC 0 CTGACGCAAATCAAAGACCTTTTAAGAA 0 - ILLUMINA NA 172 TRUE +SMAD4_15 SMAD4_15.chr18.48604668.48604754 SMAD4_15.chr18.48604668.48604754_tile_1 Homo sapiens hg19 chr18 48604668 48604754 - GCATGGTATGAAGTACTTCGTCTAGGA 0 AAGGTCATCAACACCAATTCCAGCAG 0 - ILLUMINA NA 172 TRUE +STK11_1 STK11_1.chr19.1207021.1207092 STK11_1.chr19.1207021.1207092_tile_1 Homo sapiens hg19 chr19 1207021 1207092 - CGCAACTTCTTCTTCTTGAGGATCTTG 0 TAGATGACCTCGGTGGAGTCGATGCGG 0 - ILLUMINA NA 178 TRUE +STK11_4 STK11_4.chr19.1220487.1220502 STK11_4.chr19.1220487.1220502_tile_1 Homo sapiens hg19 chr19 1220487 1220502 - AAAGCCGGGGAGCCCTGGCTGGTC 0 AGATTTTGAGGGTGCCACCGGTGGTG 0 - ILLUMINA NA 181 TRUE +STK11_8 STK11_8.chr19.1221264.1221319 STK11_8.chr19.1221264.1221319_tile_1 Homo sapiens hg19 chr19 1221264 1221319 + TGTACCCCTTCGAAGGGGACAACATCTA 0 GCTTTTGTGCAGAAATGTAGGGTTGG 0 + ILLUMINA NA 177 TRUE +STK11_12 STK11_12.chr19.1223059.1223125 STK11_12.chr19.1223059.1223125_tile_1 Homo sapiens hg19 chr19 1223059 1223125 - ACATCCTGGCCGAGTCAGCAGAGCC 0 ACCGGTCCTTGGTGTCTGGGCTC 0 - ILLUMINA NA 188 TRUE +JAK3_1 JAK3_1.chr19.17945696.17945696 JAK3_1.chr19.17945696.17945696_tile_1 Homo sapiens hg19 chr19 17945696 17945696 - ATCCCTGATCCCACTTTCATTCCCTCA 0 ATGCCCATCAGTGCCCTGGATCCTG 0 - ILLUMINA NA 176 TRUE +JAK3_2 JAK3_2.chr19.17948009.17948009 JAK3_2.chr19.17948009.17948009_tile_1 Homo sapiens hg19 chr19 17948009 17948009 - TAGTGCTGTGTGCACTAATGGCAGACT 0 AGCTTGATGAGCCAAGTGTCGTAC 0 - ILLUMINA NA 190 TRUE +SRC SRC.chr20.36031762.36031762 SRC.chr20.36031762.36031762_tile_1 Homo sapiens hg19 chr20 36031762 36031762 - AAAGAGGAAGGGCCTCGCCCCTGGCAAT 0 TACTGGGGCTCGGTGGACGTGAAGTAG 0 - ILLUMINA NA 191 TRUE +GNAS1 GNAS1.chr20.57484420.57484421 GNAS1.chr20.57484420.57484421_tile_1 Homo sapiens hg19 chr20 57484420 57484421 - ACAGCTGGTTATTCCAGAGGGACTGGG 0 GCGAAGCAGGTCCTGAAACAAAATTGA 0 - ILLUMINA NA 172 TRUE +SMARCB1_1 SMARCB1_1.chr22.24133967.24133990 SMARCB1_1.chr22.24133967.24133990_tile_1 Homo sapiens hg19 chr22 24133967 24133990 - GCGAGTGGTTTTGAAACAGGTTTACA 0 ACATACGGAGGTAGTTTCCCACCTAT 0 - ILLUMINA NA 189 TRUE +SMARCB1_3 SMARCB1_3.chr22.24143240.24143240 SMARCB1_3.chr22.24143240.24143240_tile_1 Homo sapiens hg19 chr22 24143240 24143240 - TTGTGGGGAGCACAAGGTCAAAGCAG 0 ATGCGGTTCCTGTTGATGGTTGTGGA 0 - ILLUMINA NA 175 TRUE +SMARCB1_4 SMARCB1_4.chr22.24145582.24145582 SMARCB1_4.chr22.24145582.24145582_tile_1 Homo sapiens hg19 chr22 24145582 24145582 - ATGTCCTGCGTGTCAGGTCCAGAATCT 0 TTCTGCCCATCGATCTCCATGTCCAG 0 - ILLUMINA NA 176 TRUE +SMARCB1_5_6 SMARCB1_5_6.chr22.24176352.24176357 SMARCB1_5_6.chr22.24176352.24176357_tile_1 Homo sapiens hg19 chr22 24176352 24176357 - ACTCCACCCCCACCCGATCCTCAGGA 0 TGTTGGCAAGACGCCTCATCCGCCTGG 0 - ILLUMINA NA 173 TRUE +GNA11_4 GNA11_4.chr19.3114942.3115070 GNA11_4.chr19.3114942.3115070_tile_1 Homo sapiens hg19 chr19 3114942 3115070 + AGTGCGCGGTCCACCCCCTCCT 0 CTGCCCACCCAGCAGGACGTGCT 0 + ILLUMINA NA 182 TRUE +GNA11_4 GNA11_4.chr19.3114942.3115070 GNA11_4.chr19.3114942.3115070_tile_2 Homo sapiens hg19 chr19 3114942 3115070 - CGGCACACCGGGCAAATGAGCC 0 TAGCCCAAGGTGGCGATGCGGTC 0 - ILLUMINA NA 177 TRUE +GNA11_5 GNA11_5.chr19.3118922.3119051 GNA11_5.chr19.3118922.3119051_tile_1 Homo sapiens hg19 chr19 3118922 3119051 + TCCTGCTCCAGCCGATGTCAGTCT 0 GATCCACTGCTTTGAGAACGTGACAT 0 + ILLUMINA NA 189 TRUE +GNA11_6 GNA11_6.chr19.3119204.3119357 GNA11_6.chr19.3119204.3119357_tile_2 Homo sapiens hg19 chr19 3119204 3119357 + GGATGGAGGAGAGCAAAGCCCTGTT 0 CATGGGGAGGGGCTCGCGGGCA 0 + ILLUMINA NA 189 TRUE +GNA11_7 GNA11_7.chr19.3120987.3121177 GNA11_7.chr19.3120987.3121177_tile_1 Homo sapiens hg19 chr19 3120987 3121177 - AACATCTTCAGGATGAACTCCCGCGCC 0 ACGGCCCACCCAGCTCGACCCCC 0 - ILLUMINA NA 172 TRUE +GNA11_7 GNA11_7.chr19.3120987.3121177 GNA11_7.chr19.3120987.3121177_tile_2 Homo sapiens hg19 chr19 3120987 3121177 + AGGTCCCCAGCGGGACGCCCAG 0 CAGCTCAACCTCAAGGAGTACAACCT 0 + ILLUMINA NA 187 TRUE +GNA11_7 GNA11_7.chr19.3120987.3121177 GNA11_7.chr19.3120987.3121177_tile_3 Homo sapiens hg19 chr19 3120987 3121177 - AAAAATCTCCTCCCGCGGGCAGAG 0 AGGATGGTGTCCTTCACGGCCGC 0 - ILLUMINA NA 185 TRUE +GNAQ_4 GNAQ_4.chr9.80412436.80412564 GNAQ_4.chr9.80412436.80412564_tile_1 Homo sapiens hg19 chr9 80412436 80412564 - CATTCTCATTGTGTCTTCCCTCCTCTA 0 GTAACTGAGTCCATGAAACCTATTTCC 0 - ILLUMINA NA 188 TRUE +GNAQ_5 GNAQ_5.chr9.80409379.80409508 GNAQ_5.chr9.80409379.80409508_tile_1 Homo sapiens hg19 chr9 80409379 80409508 - GCTTAGTGAATATGATCAAGTTCTCGTGG 0 GCTTTCTTGAAATTTGATTTTAGGACTTTT 0 - ILLUMINA NA 174 TRUE +GNAQ_5 GNAQ_5.chr9.80409379.80409508 GNAQ_5.chr9.80409379.80409508_tile_2 Homo sapiens hg19 chr9 80409379 80409508 + AGATAATAAAATGATAATCCATTGCCTGTC 0 TTGGCCCCCTACATCGACCATTCT 0 + ILLUMINA NA 177 TRUE +GNAQ_5 GNAQ_5.chr9.80409379.80409508 GNAQ_5.chr9.80409379.80409508_tile_3 Homo sapiens hg19 chr9 80409379 80409508 - ATTGAATTGACTTGGATGATCATCGTC 0 GGTCAGAGAGAAGAAAATGGATACACT 0 - ILLUMINA NA 182 TRUE +GNAQ_6 GNAQ_6.chr9.80343430.80343583 GNAQ_6.chr9.80343430.80343583_tile_1 Homo sapiens hg19 chr9 80343430 80343583 - GAAAATCATGTATTCCCATCTAGTCGACT 0 TTGCCCTGTGCAGCCTGCGTGTTGA 0 - ILLUMINA NA 172 TRUE +GNAQ_6 GNAQ_6.chr9.80343430.80343583 GNAQ_6.chr9.80343430.80343583_tile_2 Homo sapiens hg19 chr9 80343430 80343583 + TTCACAGCTACTGAGCTGTGGTATGA 0 AGGGGTATGTGATAATTGTTCTAAAGAGAG 0 + ILLUMINA NA 171 TRUE +GNAQ_6 GNAQ_6.chr9.80343430.80343583 GNAQ_6.chr9.80343430.80343583_tile_3 Homo sapiens hg19 chr9 80343430 80343583 - GGTCGTATACAAAAGATGGGTTGGACTTAT 0 GTTCCAGAACTCCTCGGTTATTCTGTT 0 - ILLUMINA NA 187 TRUE +GNAQ_7 GNAQ_7.chr9.80336240.80336429 GNAQ_7.chr9.80336240.80336429_tile_1 Homo sapiens hg19 chr9 80336240 80336429 - ACCATCCTCCAGTTGAACCTGAAGG 0 TTTATTGCCGTCCTGGACTCTGTGTGAGCG 0 - ILLUMINA NA 172 TRUE +GNAQ_7 GNAQ_7.chr9.80336240.80336429 GNAQ_7.chr9.80336240.80336429_tile_2 Homo sapiens hg19 chr9 80336240 80336429 + CAGGGAAGGGCAGGGCGGGTGTCTA 0 ATAATTTTGTCACTGTCTGGGTTCAGG 0 + ILLUMINA NA 172 TRUE +GNAQ_7 GNAQ_7.chr9.80336240.80336429 GNAQ_7.chr9.80336240.80336429_tile_3 Homo sapiens hg19 chr9 80336240 80336429 - CCAATGATGATTGAATACATTAGCAGAT 0 TACTCCCACTTCACGTGCGCCACAGAC 0 - ILLUMINA NA 177 TRUE +[Targets] +TargetA TargetB Target Number Chromosome Start Position End Position Probe Strand Sequence Species Build ID +MPL1_2.chr1.43815008.43815009_tile_1 MPL1_2.chr1.43815008.43815009_tile_1 1 chr1 43814982 43815163 + GGTGGCAGTTTCCTGCACACTACAGGTACCGCCCCCGCCAGGCAGGAGACTGGCGGTGGACCAGGTGGAGCCGAAGGCCTGTAAACAGGCATTCTTGGTTCGCTCTGTGACCCCAGATCTCCGTCCACCGCC Homo sapiens hg19 +NRAS1_7.chr1.115256528.115256531_tile_1 NRAS1_7.chr1.115256528.115256531_tile_1 1 chr1 115256500 115256680 + TCTTGTCCAGCTGTATCCAGTATGTCCAACAAACAGGTTTCACCATCTATAACCACTTGTTTTCTGTAAGAATCCTGGGGGTGTGGAGGGTAAGGGGGCAGGGAGGGAGGGAAGTTCAATTTTTATTA Homo sapiens hg19 +NRAS8_13.chr1.115258730.115258748_tile_1 NRAS8_13.chr1.115258730.115258748_tile_1 1 chr1 115258702 115258884 + TGCGCTTTTCCCAACACCACCTGCTCCAACCACCACCAGTTTGTACTCAGTCATTTCACACCAGCAAGAACCTGTTGGAAACCAGTAATCAGGGTTAATTGGCGAGCCACATCTACAGTACTTTAAAG Homo sapiens hg19 +ALK1.chr2.29432664.29432664_tile_1 ALK1.chr2.29432664.29432664_tile_1 1 chr2 29432636 29432822 + TCGGGCCATCCCGAAGTCTCCAATCTTGGCCACTCTTCCAGGGCCTGGACAGGTCAAGAGGCAGTTTCTGGCAGCAATGTCTCTGGGAAGAAAGGAAATGCATTTCCTAATTTTATCCCTAGGAAGATGAGTG Homo sapiens hg19 +ALK2.chr2.29443695.29443695_tile_1 ALK2.chr2.29443695.29443695_tile_1 1 chr2 29443667 29443836 + GTTGAATTTGCTGCAGAGCAGAGAGGGATGTAACCAAAATTAACTGAGCTGAGTCTGGGCAAATCTTAAACTGGGAGGAACAGGATACAAAGTTACATTTTCAGCAGCTACAATGTATA Homo sapiens hg19 +IDH1_1_2.chr2.209113112.209113113_tile_1 IDH1_1_2.chr2.209113112.209113113_tile_1 1 chr2 209113084 209113264 + ACGACCTATGATGATAGGTTTTACCCATCCACTCACAAGCCGGGGGATATTTTTGCAGATAATGGCTTCTCTGAAGACCGTGCCACCCAGAATATTTCGTATGGTGCCATTTGGTGATTTCCACATT Homo sapiens hg19 +ERBB4_1_2.chr2.212288942.212288955_tile_1 ERBB4_1_2.chr2.212288942.212288955_tile_1 1 chr2 212288912 212289100 + CCTTTCTCTAATAAATCAGGGATTTCTCGCGTTGGAATTCCATCATAGGGTTTTCCTCCAAAGGTCATCAGTTCCCATATAGTAACTCCTATATTGGAGAAAAAATTCTTACTTAAGCATATTAACAACATATGT Homo sapiens hg19 +ERBB4_3_4.chr2.212530066.212530135_tile_1 ERBB4_3_4.chr2.212530066.212530135_tile_1 1 chr2 212530036 212530210 + TGGATGGCATGGGTGGCACTCCCGATCTGGATCAGCATACTTGAAAATGAAACTGTTTGCCCCCTGTAAGCCATCTGGACATTTTTCCACACAGTTTGGGCCATCTTTAAAATGAGAGCACT Homo sapiens hg19 +ERBB4_5.chr2.212576857.212576857_tile_1 ERBB4_5.chr2.212576857.212576857_tile_1 1 chr2 212576821 212576990 + AATCCACAGTCTGAGCTGACATCAATGATCCTGTGCCAATGCCATCACAAGCTGTAGAAACAAGACTCAGAGTTAGGGGATTGAGAAACTTATTTTTGGCCAATAAATCA Homo sapiens hg19 +ERBB4_6_7.chr2.212578341.212578349_tile_1 ERBB4_6_7.chr2.212578341.212578349_tile_1 1 chr2 212578315 212578499 + CGCACACAAGAACTGGAATCTACCACAAAGTTATCTGATTAAAAAAAAAAAAAAGGTAAAATAAGCATTAATGTTAACATTCAGCAAACAAGCTCAAAACAAGATATTTTAGGGTTTAAAAATGATTAGCA Homo sapiens hg19 +ERBB4_8.chr2.212587147.212587147_tile_1 ERBB4_8.chr2.212587147.212587147_tile_1 1 chr2 212587115 212587285 + CTCCATATGTGTACTTTGCATTGAAATTGTGCTCCAGTTGAAAGGTGGTTGGATTGTAGACAAAGGTTTGGGGACACTGAGTAACACATGCTCCACTGTCATTGAAATTCATGCAGG Homo sapiens hg19 +ERBB4_9.chr2.212589811.212589811_tile_1 ERBB4_9.chr2.212589811.212589811_tile_1 1 chr2 212589783 212589957 + TGTGTCCTTAGGTCCTGAGCAGCCTCCAGCACATTCTCGATGGCAGCAGTCACTGACGTAAGGTCCGTAGCATCTGCCGTCACATTGTTCTGCACACACCGTCCTTGTCACTGCAGAAGAC Homo sapiens hg19 +ERBB4_10.chr2.212652764.212652764_tile_1 ERBB4_10.chr2.212652764.212652764_tile_1 1 chr2 212652706 212652876 + ATAATTCTACTTACATCCTGAACTACCATTTGTTGACACAAGAGTCAAGTTGGAAGGCCATGGGTTCCGAACAATATCTTGCCAATGAATGGTGTCTGCATAACAAAGGAATTT Homo sapiens hg19 +ERBB4_11.chr2.212812157.212812157_tile_1 ERBB4_11.chr2.212812157.212812157_tile_1 1 chr2 212812127 212812311 + TGTCAAGTTCTTTAATCCAAGTTCTTGAAGTCCAAAGTTTCCATCTTTTCTGTAGTTTAAAAATATTGCCAAGGCATATCGATCCTCATAAAGTTTTGTCCCACGAATAATGCGTAAATTCTCCAGAGG Homo sapiens hg19 +VHL1_2.chr3.10183797.10183817_tile_1 VHL1_2.chr3.10183797.10183817_tile_1 1 chr3 10183769 10183952 + GGCTCAACTTCGACGGCGAGCCGCAGCCCTACCCAACGCTGCCGCCTGGCACGGGCCGCCGCATCCACAGCTACCGAGGTACGGGCCCGGCGCTTAGGCCCGACCCAGCAGGGACGATAGCACGGTCTGAAGC Homo sapiens hg19 +VHL3_5.chr3.10188245.10188301_tile_1 VHL3_5.chr3.10188245.10188301_tile_1 1 chr3 10188217 10188401 + GGTTAACCAAACTGAATTATTTGTGCCATCTCTCAATGTTGACGGACAGCCTATTTTTGCCAATATCACACTGCCAGGTACTGACGTTTTACTTTTTAAAAAGATAAGGTTGTTGTGGTAAGTACAGGATA Homo sapiens hg19 +VHL6_8.chr3.10191480.10191506_tile_1 VHL6_8.chr3.10191480.10191506_tile_1 1 chr3 10191450 10191634 + TCTGAAAGAGCGATGCCTCCAGGTTGTCCGGAGCCTAGTCAAGCCTGAGAATTACAGGAGACTGGACATCGTCAGGTCGCTCTACGAAGATCTGGAAGACCACCCAAATGTGCAGAAAGACCTGGAGCGG Homo sapiens hg19 +MLH1.chr3.37067240.37067240_tile_1 MLH1.chr3.37067240.37067240_tile_1 1 chr3 37067212 37067394 + GGTTCGTACAGATTCCCGGGAACAGAAGCTTGATGCATTTCTGCAGCCTCTGAGCAAACCCCTGTCCAGTCAGCCCCAGGCCATTGTCACAGAGGATAAGACAGATATTTCTAGTGGCAGGGCTAGGCAG Homo sapiens hg19 +CTNNB1_1_16.chr3.41266040.41266137_tile_1 CTNNB1_1_16.chr3.41266040.41266137_tile_1 1 chr3 41266010 41266180 + ATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGC Homo sapiens hg19 +PIK3CA1.chr3.178916876.178916876_tile_1 PIK3CA1.chr3.178916876.178916876_tile_1 1 chr3 178916836 178917024 + TGATGAAACAAGACGACTTTGTGACCTTCGGCTTTTTCAACCCTTTTTAAAAGTAATTGAACCAGTAGGCAACCGTGAAGAAAAGATCCTCAATCGAGAAATTGGTATGATACAATATCCTATTCTAAAATGCAAA Homo sapiens hg19 +PIK3CA2.chr3.178921553.178921553_tile_1 PIK3CA2.chr3.178921553.178921553_tile_1 1 chr3 178921525 178921709 + ATGTAAATATTCGAGACATTGATAAGGTAAAGTCAAATGCTGATGCTTATTATTTTATAGAAATTATTTTAGATAACCTTTTTCTTGCACTATACAGTAATCTGTTGACCTGTAGTATGTTTTCAGATGGT Homo sapiens hg19 +PIK3CA3.chr3.178927980.178927980_tile_1 PIK3CA3.chr3.178927980.178927980_tile_1 1 chr3 178927906 178928082 + TTATAATTTAGACTAGTGAATATTTTTCTTTGTTTTTTAAGGAACACTGTCCATTGGCATGGGGAAATATAAACTTGTTTGATTACACAGACACTCTAGTATCTGGAAAAATGGCTTTGAATC Homo sapiens hg19 +PIK3CA4_11.chr3.178936074.178936095_tile_1 PIK3CA4_11.chr3.178936074.178936095_tile_1 1 chr3 178936044 178936214 + ATCCTCTCTCTGAAATCACTGAGCAGGAGAAAGATTTTCTATGGAGTCACAGGTAAGTGCTAAAATGGAGATTCTCTGTTTCTTTTTCTTTATTACAGAAAAAATAACTGAATTTGG Homo sapiens hg19 +PIK3CA12.chr3.178938860.178938860_tile_1 PIK3CA12.chr3.178938860.178938860_tile_1 1 chr3 178938832 178939004 + CACCTGAATAGGCAAGTCGAGGCAATGGAAAAGCTCATTAACTTAACTGACATTCTCAAACAGGAGAAGAAGGATGAAACACAAAAGGTGTGTGACTCTAGTTTGTGTTTGAGACTCTT Homo sapiens hg19 +PIK3CA13_20.chr3.178952007.178952150_tile_1 PIK3CA13_20.chr3.178952007.178952150_tile_1 1 chr3 178951881 178952054 + TATCTAGCTATTCGACAGCATGCCAATCTCTTCATAAATCTTTTCTCAATGATGCTTGGCTCTGGAATGCCAGAACTACAATCTTTTGATGACATTGCATACATTCGAAAGACCCTAGCC Homo sapiens hg19 +PIK3CA13_20.chr3.178952007.178952150_tile_2 PIK3CA13_20.chr3.178952007.178952150_tile_2 1 chr3 178951999 178952184 - TTTCAGTTCAATGCATGCTGTTTAATTGTGTGGAAGATCCAATCCATTTTTGTTGTCCAGCCACCATGATGTGCATCATTCATTTGTTTCATGAAATACTCCAAAGCCTCTTGCTCAGTTTTATCTAAG Homo sapiens hg19 +FGFR3_1_2.chr4.1803564.1803568_tile_1 FGFR3_1_2.chr4.1803564.1803568_tile_1 1 chr4 1803538 1803712 + GCGCTCCCCGCACCGGCCCATCCTGCAGGCGGGGCTGCCGGCCAACCAGACGGCGGTGCTGGGCAGCGACGTGGAGTTCCACTGCAAGGTGTACAGTGACGCACAGCCCCACATCCAGTGGCT Homo sapiens hg19 +FGFR3_3_4.chr4.1806119.1806153_tile_1 FGFR3_3_4.chr4.1806119.1806153_tile_1 1 chr4 1806091 1806277 + CGGGGTGGGCTTCTTCCTGTTCATCCTGGTGGTGGCGGCTGTGACGCTCTGCCGCCTGCGCAGCCCCCCCAAGAAAGGCCTGGGCTCCCCCACCGTGCACAAGATCTCCCGCTTCCCGCTCAAGCGACAGGTA Homo sapiens hg19 +FGFR3_5_7.chr4.1807862.1807890_tile_1 FGFR3_5_7.chr4.1807862.1807890_tile_1 1 chr4 1807836 1808025 + CCGGGACGTGCACAACCTCGACTACTACAAGAAGACGACCAACGTGAGCCCGGCCCTGGGGTGCGGGGGTGGGGGTCATGCCAGTAGGACGCCTGGCGCCAACACCGCCTTCCCACACCCTCCCAGGGCCGGCTGCCCGTGA Homo sapiens hg19 +FGFR3_8.chr4.1808331.1808331_tile_1 FGFR3_8.chr4.1808331.1808331_tile_1 1 chr4 1808295 1808464 + GCTCCCCGTACCCCGGCATCCCTGTGGAGGAGCTCTTCAAGCTGCTGAAGGAGGGCCACCGCATGGACAAGCCCGCCAACTGCACACACGACCTGTGAGTGGCATCCCTGGCCCTCCACTGGGTCC Homo sapiens hg19 +FGFR3_9.chr4.1808949.1808949_tile_1 FGFR3_9.chr4.1808949.1808949_tile_1 1 chr4 1808921 1809105 + CCTGCTGCCCCCGGCCCCACCCAGCAGTGGGGGCTCGCGGACGTGAAGGGCCACTGGTCCCCAACAATGTGAGGGGTCCCTAGCAGCCCACCCTGCTGCTGGTGCACAGCCACTCCCCGGCATGAGACTCAGTGC Homo sapiens hg19 +PDGFRA1_4.chr4.55141013.55141049_tile_1 PDGFRA1_4.chr4.55141013.55141049_tile_1 1 chr4 55140981 55141157 + AAACCGAGGTATGAAATTCGCTGGAGGGTCATTGAATCAATCAGCCCAGATGGACATGAATATATTTATGTGGACCCGATGCAGCTGCCTTATGACTCAAGATGGGAGTTTCCAAGAGATGGA Homo sapiens hg19 +PDGFRA5.chr4.55144146.55144146_tile_1 PDGFRA5.chr4.55144146.55144146_tile_1 1 chr4 55144120 55144306 + AACTTGCTGGGAGCCTGCACCAAGTCAGGTGGGCTCACTGACCTGGAGTGAGGATTTTCACTGGACACATGTGGTTGTGAAAACTGTTCAATCAGGCTTAAATCCTCCACTCTCCATCCCCACACATGGCAGGG Homo sapiens hg19 +PDGFRA6.chr4.55144547.55144547_tile_1 PDGFRA6.chr4.55144547.55144547_tile_1 1 chr4 55144519 55144703 + CACAGAGTATTGCTTCTATGGAGATTTGGTCAACTATTTGCATAAGAATAGGGATAGCTTCCTGAGCCACCACCCAGAGAAGCCAAAGAAAGAGCTGGATATCTTTGGATTGAACCCTGCTGATGAAAGCAC Homo sapiens hg19 +PDGFRA7_23.chr4.55152040.55152109_tile_1 PDGFRA7_23.chr4.55152040.55152109_tile_1 1 chr4 55152012 55152184 + CGTCCTCCTGGCACAAGGAAAAATTGTGAAGATCTGTGACTTTGGCCTGGCCAGAGACATCATGCATGATTCGAACTATGTGTCGAAAGGCAGTGTACGTCCTCACTTCCCTCACTGGTCA Homo sapiens hg19 +KIT1.chr4.55561764.55561764_tile_1 KIT1.chr4.55561764.55561764_tile_1 1 chr4 55561736 55561913 + CGACGAGATTAGGCTGTTATGCACTGATCCGGGCTTTGTCAAATGGACTTTTGAGATCCTGGATGAAACGAATGAGAATAAGCAGAATGAATGGATCACGGAAAAGGCAGAAGCCACCAACACCG Homo sapiens hg19 +KIT2.chr4.55592185.55592186_tile_1 KIT2.chr4.55592185.55592186_tile_1 1 chr4 55592155 55592341 + CCTATTTTAACTTTGCATTTAAAGGTAACAACAAAGGTATATTTCTTTTTAATCCAATTTAAGGGGATGTTTAGGCTCTGTCTACCATATCAGTCATGATTTTAAGTTCATTCCAACATTGACCATGTCATTTC Homo sapiens hg19 +KIT3_19.chr4.55593464.55593689_tile_1 KIT3_19.chr4.55593464.55593689_tile_1 1 chr4 55593342 55593512 + ATTTCTCTTCCATTGTAGAGCAAATCCATCCCCACACCCTGTTCACTCCTTTGCTGATTGGTTTCGTAATCGTAGCTGGCATGATGTGCATTATTGTGATGATTCTGACCTACAAATA Homo sapiens hg19 +KIT3_19.chr4.55593464.55593689_tile_2 KIT3_19.chr4.55593464.55593689_tile_2 1 chr4 55593436 55593609 - TTCTGTGGGGAGAAAGGGAAAAATAGATCACCTTTTAATAATTATTGTCTCAGTCATTAGAGCACTCTGGAGAGAGAACAAATAAATGGTTACCTGTAAATATTTGTAGGTCAGAATCATCA Homo sapiens hg19 +KIT3_19.chr4.55593464.55593689_tile_3 KIT3_19.chr4.55593464.55593689_tile_3 1 chr4 55593556 55593739 + AACCCATGTATGAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTTCCTTATGATCACAAATGGGAGTTTCCCAGAAACAGGCTGAGTTTTGGTCAG Homo sapiens hg19 +KIT20_21.chr4.55594221.55594258_tile_1 KIT20_21.chr4.55594221.55594258_tile_1 1 chr4 55594193 55594380 + CAAAGTCCTGAGTTACCTTGGTAATCACATGAATATTGTGAATCTACTTGGAGCCTGCACCATTGGAGGTAAAGCCGTGTCCAAGCTGCCTTTTATTGTCTGTCAGGTTATCAAAACATGACATTTTAATATG Homo sapiens hg19 +KIT22.chr4.55595519.55595519_tile_1 KIT22.chr4.55595519.55595519_tile_1 1 chr4 55595493 55595675 + CAGAATATTGTTGCTATGGTGATCTTTTGAATTTTTTGAGAAGAAAACGTGATTCATTTATTTGTTCAAAGCAGGAAGATCATGCAGAAGCTGCACTTTATAAGAATCTTCTGCATTCAAAGGAGTCT Homo sapiens hg19 +KIT23.chr4.55597495.55597497_tile_1 KIT23.chr4.55597495.55597497_tile_1 1 chr4 55597467 55597652 + CAGCGATAGTACTAATGAGTACATGGACATGAAACCTGGAGTTTCTTATGTTGTCCCAACCAAGGCCGACAAAAGGAGATCTGTGAGAATAGGTGAGTACCTACCTATCAAGCAACCAAGAGTAACTTTAC Homo sapiens hg19 +KIT24_28.chr4.55599320.55599348_tile_1 KIT24_28.chr4.55599320.55599348_tile_1 1 chr4 55599290 55599472 + AGAGACATCAAGAATGATTCTAATTATGTGGTTAAAGGAAACGTGAGTACCCATTCTCTGCTTGACAGTCCTGCAAAGGATTTTTAGTTTCAACTTTCGATAAAAATTGTTTCCTGTGATTTTCATAAT Homo sapiens hg19 +KIT29.chr4.55602694.55602694_tile_1 KIT29.chr4.55602694.55602694_tile_1 1 chr4 55602666 55602850 + CCTGAAAGCATTTTCAACTGTGTATACACGTTTGAAAGTGACGTCTGGTCCTATGGGATTTTTCTTTGGGAGCTGTTCTCTTTAGGTAAAATGATCCTTGCCAAAGACAACTTCATTAGACTCAGAGCATCTT Homo sapiens hg19 +KDR1.chr4.55946114.55946257_tile_1 KDR1.chr4.55946114.55946257_tile_1 1 chr4 55945984 55946155 + CGGCTACTTCCTGCTGGTGGAAAGAACAACACTTGAAAATCTGAGCAGCACCTCTCATGTGATGTCCAGGAGTTGGGGGTGTGGATGCTTCCTTTTAAACAGGAGGAGAGCT Homo sapiens hg19 +KDR1.chr4.55946114.55946257_tile_2 KDR1.chr4.55946114.55946257_tile_2 1 chr4 55946098 55946284 - GGATATCACTCCGATGACACAGACACCACCGTGTACTCCAGTGAGGAAGCAGAACTTTTAAAGCTGATAGAGATTGGAGTGCAAACCGGTAGCACAGCCCAGATTCTCCAGCCTGACTCGGGGACCACACTGA Homo sapiens hg19 +KDR3.chr4.55953807.55953807_tile_1 KDR3.chr4.55953807.55953807_tile_1 1 chr4 55953777 55953965 + TTGGGGTCACATACTTCCTCCTCCTCCATACAGGAAACAGGTGAGGTAGGCAGAGAGAGTCCAGAATCCTCTTCCATGCTCAAAGTCTCTGATATCGGAAGAACAATGTAGTCTTTGCCATCCTGAAACAATAAA Homo sapiens hg19 +KDR4.chr4.55955111.55955127_tile_1 KDR4.chr4.55955111.55955127_tile_1 1 chr4 55955085 55955257 + CCCCGTGCCAGCAGTCCAGCATGGTCTGGTACCTAGAGAAGCAAAACACTGATTTCATTAAATGCCTCTTTCTTCCTGAATGCTGAAAATAAGCACTTAAATGAGTACACATTTGTAAAGAG Homo sapiens hg19 +KDR6.chr4.55960989.55961023_tile_1 KDR6.chr4.55960989.55961023_tile_1 1 chr4 55960959 55961129 + TCACTGAGGGACTTCTCCTCCACAAATCCAGAGCTGGCTGAGCTCTGGCTACTGGTGATGCTGTCCAAGCGCCGTTTCAGATCCACAGGGATTGCTCCAACGTAGTCTTTCCCTTGA Homo sapiens hg19 +KDR8.chr4.55962507.55962507_tile_1 KDR8.chr4.55962507.55962507_tile_1 1 chr4 55962477 55962653 + GCTCCTTCTACAAATACAGTACAAAGAGGGAAATCATAGGTATGGACATTTCCTTCAATAATTGGGGTCCCTCCCTCCCTGCATGCCACTATACAACTTACCCTCCGGGGTAACACAGCTGTGA Homo sapiens hg19 +KDR9.chr4.55972964.55972964_tile_1 KDR9.chr4.55972964.55972964_tile_1 1 chr4 55972936 55973106 + ACTGAGACAGCTTGGCTATAAGAAAGAGATAACAGCGCATATTATGATTTAATTTTTCTTTAATTAGAGTCAAGAGTAAGGAAAAGATTCAGACTTTGGTTATTCTGTTCTTAGAAA Homo sapiens hg19 +KDR10.chr4.55979623.55979623_tile_1 KDR10.chr4.55979623.55979623_tile_1 1 chr4 55979595 55979775 + CTCGGTTTACAAGTTTCTTATGCTGATGCTGAAAAAAAGAGTTGACTGAACTTCCAAAGCACAGCATATAACATTACCCAATAACTTCTAGTAACACACAGAATTAAATCTGGGCTTTGGTAAACATT Homo sapiens hg19 +KDR11.chr4.55980348.55980348_tile_1 KDR11.chr4.55980348.55980348_tile_1 1 chr4 55980320 55980496 + TGCTGTACAATTTAAGACAAGCTTTTCTCCAACAGATAGTTCAATTCCATGAGACGGACTCAGAACCACATCATAAATCCTATACCCTAGAGCAAGTAAATTGAAAAAACAGAACATGAGAGA Homo sapiens hg19 +FBXW7_1.chr4.153245446.153245446_tile_1 FBXW7_1.chr4.153245446.153245446_tile_1 1 chr4 153245416 153245604 + AACGACTGGTGCCCTGTTAACGTGTGAATGCAATTCCCTGTCTCCACATCCCAAACACGGATTGATGTATCAAGAGATCCACTCACCACATGGATACCATCAAACTACAAAAGACACAGTTTATTAGAATAGA Homo sapiens hg19 +FBXW7_2.chr4.153247288.153247366_tile_1 FBXW7_2.chr4.153247288.153247366_tile_1 1 chr4 153247248 153247417 + TTGAACACAGCGGACTGCTGCAACATGACCCATCAAAACATGTAAACACTGGCCTGTCTCAATATCCCAAACCCTAAGAGTGGCATCTCGAGAACCGCTAACAACTCTGCAG Homo sapiens hg19 +FBXW7_5.chr4.153249384.153249384_tile_1 FBXW7_5.chr4.153249384.153249384_tile_1 1 chr4 153249338 153249520 + TTCATGAAGATGCATACAACGCACAGTGGAAGTATGCCCATATAAGGTGTGTATACATTCTCCAGTCTCTGCATTCCACACTTTGAGTGTCCGATCTGTAGATCCACTAATGATGATGTTGTCTCTCAT Homo sapiens hg19 +FBXW7_7.chr4.153250883.153250883_tile_1 FBXW7_7.chr4.153250883.153250883_tile_1 1 chr4 153250853 153251031 + ATTCGGTTACCACAAAACTGTAAGCATGTGATCACATGATCATCATGTCCTTTCAGCACCTATAAGAAAGATGTGCAGATTAGAAATATGTTAATTAAATTATGTTCTTTAAAATACTGGTGAAGA Homo sapiens hg19 +FBXW7_8.chr4.153258983.153258983_tile_1 FBXW7_8.chr4.153258983.153258983_tile_1 1 chr4 153258953 153259142 + TCGTTGAAACTGGGGTTCTATCACTTGCATCATATGTTTTACTTGTGTTGGTTCACAACTATCAATGAGTTCATCTAAAGCAAGCAATTTCTCTGGTCCACTCCAGCTCTATCAAAGAGAATTAGAAATTTT Homo sapiens hg19 +APC1.chr5.112173917.112173917_tile_1 APC1.chr5.112173917.112173917_tile_1 1 chr5 112173887 112174071 + AAGCGAGGTTTGCAGATCTCCACCACTGCAGCCCAGATTGCCAAAGTCATGGAAGAAGTGTCAGCCATTCATACCTCTCAGGAAGACAGAAGTTCTGGGTCTACCACTGAATTACATTGTGTGACAGATGA Homo sapiens hg19 +APC2.chr5.112174631.112174631_tile_1 APC2.chr5.112174631.112174631_tile_1 1 chr5 112174603 112174775 + TCGAGTGGGTTCTAATCATGGAATTAATCAAAATGTAAGCCAGTCTTTGTGTCAAGAAGATGACTATGAAGATGATAAGCCTACCAATTATAGTGAACGTTACTCTGAAGAAGAACAGC Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_1 APC3_42.chr5.112175162.112175958_tile_1 1 chr5 112175034 112175208 - TCTGCTTCCTGTGTCGTCTGATTACATCCTATTTCATCTTCAGCTGATGACAAAGATGATAATGAACTACATCTTGAAAAACATATTGGAGTATCTTCTACACAATAAGTCTGTATTGTT Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_2 APC3_42.chr5.112175162.112175958_tile_2 1 chr5 112175128 112175297 + ATGTAATCAGACGACACAGGAAGCAGATTCTGCTAATACCCTGCAAATAGCAGAAATAAAAGAAAAGATTGGAACTAGGTCAGCTGAAGATCCTGTGAGCGAAGTTCCAGCAGTGTCAC Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_3 APC3_42.chr5.112175162.112175958_tile_3 1 chr5 112175216 112175386 - CCTGAAGAAAATTCAACAGCTTTGTGCCTGGCTGATTCTGAAGATAAACTAGAACCCTGCAGTCTGCTGGATTTGGTTCTAGGGTGCTGTGACACTGCTGGAACTTCGCTCACAGGAT Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_4 APC3_42.chr5.112175162.112175958_tile_4 1 chr5 112175306 112175475 + CACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCA Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_5 APC3_42.chr5.112175162.112175958_tile_5 1 chr5 112175394 112175566 - GCCACTTACCATTCCACTGCATGGTTCACTCTGAACGGAGCTGGCAATCGAACGACTCTCAAAACTATCAAGTGAACTGACAGAAGTACATCTGCTAAACATGAGTGGGGTCTCCTGAAC Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_6 APC3_42.chr5.112175162.112175958_tile_6 1 chr5 112175512 112175683 + GCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATA Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_7 APC3_42.chr5.112175162.112175958_tile_7 1 chr5 112175630 112175799 - CCGTGGCAAAATGTAATAAAGTATCAGCATCTGGAAGAACCTGGACCCTCTGAACTGCAGCATTTACTGCAGCTTGCTTAGGTCCACTCTCTCTCTTTTCAGCAGTAGGTGCTTT Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_8 APC3_42.chr5.112175162.112175958_tile_8 1 chr5 112175740 112175911 + GGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAA Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_9 APC3_42.chr5.112175162.112175958_tile_9 1 chr5 112175854 112176042 - AGTATTTCAATATCATCATCATCTGAATCATCTAATAGGTCCTTTTCAGAATCAATAGTTTTTTCTGCCTCTTTCTCTTGGTTTTCATTTGATTCTTTAGGCTGCTCTGATTCTGTTTCATTCCCATTGTCATTT Homo sapiens hg19 +CSF1R1_3.chr5.149433644.149433646_tile_1 CSF1R1_3.chr5.149433644.149433646_tile_1 1 chr5 149433616 149433799 + GATAGTTGTTGGGCTGCAGCAAGGGCTGGGCGATATCCCCTTGCTCGCAGCAGGTCAGGTGCTCACTAGAGCTCTCCTCCTCCAGCTCACTGCTGCTGCTGCCGCTGCCACCGCTTCTGCTGCTGCTCGGC Homo sapiens hg19 +CSF1R4.chr5.149453044.149453044_tile_1 CSF1R4.chr5.149453044.149453044_tile_1 1 chr5 149453016 149453189 + CAAGTAGGCACTCTCTGGAAAGCAGAACACACAAGCATCTGGCATTAGTGGGAAGATGTCCTTGTTTATTTGTCCATTTTGTCATCCACCCATTGATCCAGTCCCTGAGCAGCTATGTCAC Homo sapiens hg19 +NPM1.chr5.170837547.170837548_tile_1 NPM1.chr5.170837547.170837548_tile_1 1 chr5 170837493 170837677 + TTTTTTTTCCAGGCTATTCAAGATCTCTGGCAGTGGAGGAAGTCTCTTTAAGAAAATAGTTTAAACAATTTGTTAAAAAATTTTCCGTCTTATTTCATTTCTGTAACAGTTGATATCTGGCTGTCCTTTTTA Homo sapiens hg19 +EGFR1.chr7.55211080.55211080_tile_1 EGFR1.chr7.55211080.55211080_tile_1 1 chr7 55211052 55211238 + AGAGGAAATATGTACTACGAAAATTCCTATGCCTTAGCAGTCTTATCTAACTATGATGCAAATAAAACCGGACTGAAGGAGCTGCCCATGAGAAATTTACAGGGTGAGAGGCTGGGATGCCAAGGCTGGGGGT Homo sapiens hg19 +EGFR2.chr7.55221822.55221822_tile_1 EGFR2.chr7.55221822.55221822_tile_1 1 chr7 55221792 55221964 + GGTGCCACCTGCGTGAAGAAGTGTCCCCGTGAGTCCTCCTCTGTGGGCCCTCTAACTGGTCAGGCATCCTTGTCCCGCTCTGTCTCCTGCTGAGCCCTGGAGTATCCCATCTTGGAGAGT Homo sapiens hg19 +EGFR3.chr7.55233043.55233043_tile_1 EGFR3.chr7.55233043.55233043_tile_1 1 chr7 55233019 55233203 + GGAGTCATGGGAGAAAACAACACCCTGGTCTGGAAGTACGCAGACGCCGGCCATGTGTGCCACCTGTGCCATCCAAACTGCACCTACGGGTGAGTGGAAAGTGAAGGAGAACAGAACATTTCCTCTCTTGCAAAT Homo sapiens hg19 +EGFR4.chr7.55241677.55241708_tile_1 EGFR4.chr7.55241677.55241708_tile_1 1 chr7 55241649 55241827 + AGGAAACTGAATTCAAAAAGATCAAAGTGCTGGGCTCCGGTGCGTTCGGCACGGTGTATAAGGTAAGGTCCCTGGCACAGGCCTCTGGGCTGGGCCGCAGGGCCTCTCATGGTCTGGTGGGGAGCC Homo sapiens hg19 +EGFR9.chr7.55242418.55242511_tile_1 EGFR9.chr7.55242418.55242511_tile_1 1 chr7 55242388 55242576 + GACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTCGCTATCAAGGAATTAAGAGAAGCAACATCTCCGAAAGCCAACAAGGAAATCCTCGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCT Homo sapiens hg19 +EGFR44.chr7.55249005.55249131_tile_1 EGFR44.chr7.55249005.55249131_tile_1 1 chr7 55248879 55249052 + TCTTCACCTGGAAGGGGTCCATGTGCCCCTCCTTCTGGCCACCATGCGAAGCCACACTGACGTGCCTCTCCCTCCCTCCAGGAAGCCTACGTGATGGCCAGCGTGGACAACCCCCACGTGTG Homo sapiens hg19 +EGFR44.chr7.55249005.55249131_tile_2 EGFR44.chr7.55249005.55249131_tile_2 1 chr7 55249003 55249178 - CAGTTGAGCAGGTACTGGGAGCCAATATTGTCTTTGTGTTCCCGGACATAGTCCAGGAGGCAGCCGAAGGGCATGAGCTGCGTGATGAGCTGCACGGTGGAGGTGAGGCAGATGCCCAGCAGGCGGC Homo sapiens hg19 +EGFR54.chr7.55259514.55259524_tile_1 EGFR54.chr7.55259514.55259524_tile_1 1 chr7 55259486 55259662 + GCTGGCCAAACTGCTGGGTGCGGAAGAGAAAGAATACCATGCAGAAGGAGGCAAAGTAAGGAGGTGGCTTTAGGTCAGCCAGCATTTTCCTGACACCAGGGACCAGGCTGCCTTCCCACTAGC Homo sapiens hg19 +MET1.chr7.116339642.116339642_tile_1 MET1.chr7.116339642.116339642_tile_1 1 chr7 116339614 116339792 + AGCCCAGCCAGTGTCCTGACTGTGTGGTGAGCGCCCTGGGAGCCAAAGTCCTTTCATCTGTAAAGGACCGGTTCATCAACTTCTTTGTAGGCAATACCATAAATTCTTCTTATTTCCCAGATCAT Homo sapiens hg19 +MET2.chr7.116340262.116340262_tile_1 MET2.chr7.116340262.116340262_tile_1 1 chr7 116340234 116340420 + AACAAGATCGTCAACAAAAACAATGTGAGATGTCTCCAGCATTTTTACGGACCCAATCATGAGCACTGCTTTAATAGGGTAAGTCACATCAGTTCCCCACTTATAAACTGTGAGGTATAAATTAGAAATAAGT Homo sapiens hg19 +MET3.chr7.116411990.116411990_tile_1 MET3.chr7.116411990.116411990_tile_1 1 chr7 116411958 116412127 + GCCCAACTACAGAAATGGTTTCAAATGAATCTGTAGACTACCGAGCTACTTTTCCAGAAGGTATATTTCAGTTTATTGTTCTGAGAAATACCTATACATATACCTCAGTGGGTTGT Homo sapiens hg19 +MET4.chr7.116417463.116417464_tile_1 MET4.chr7.116417463.116417464_tile_1 1 chr7 116417431 116417620 + TATATCATGGGACTTTGTTGGACAATGATGGCAAGAAAATTCACTGTGCTGTGAAATCCTTGAACAGTAAGTGGCATTTTATTTAACCATGGAGTATACTTTTGTGGTTTGCAACCTAATAAATAGCTTATAATA Homo sapiens hg19 +MET6.chr7.116423413.116423474_tile_1 MET6.chr7.116423413.116423474_tile_1 1 chr7 116423385 116423555 + TGTATGATAAAGAATACTATAGTGTACACAACAAAACAGGTGCAAAGCTGCCAGTGAAGTGGATGGCTTTGGAAAGTCTGCAAACTCAAAAGTTTACCACCAAGTCAGATGTGGTAAT Homo sapiens hg19 +SMO1.chr7.128845101.128845101_tile_1 SMO1.chr7.128845101.128845101_tile_1 1 chr7 128845073 128845257 + GGTTCGGACAGACAACCCCAAGAGCTGGTACGAGGACGTGGAGGGCTGCGGCATCCAGTGCCAGAACCCGCTCTTCACAGAGGCTGAGCACCAGGACATGCACAGCTACATCGCGGCCTTCGGGGCCGTCACGGGC Homo sapiens hg19 +SMO2.chr7.128846040.128846040_tile_1 SMO2.chr7.128846040.128846040_tile_1 1 chr7 128846010 128846194 + TACGCCCTGATGGCTGGTGTGGTTTGGTTTGTGGTCCTCACCTATGCCTGGCACACTTCCTTCAAAGCCCTGGGCACCACCTACCAGCCTCTCTCGGGCAAGACCTCCTACTTCCACCTGCTCACCTGGTC Homo sapiens hg19 +SMO3.chr7.128846374.128846374_tile_1 SMO3.chr7.128846374.128846374_tile_1 1 chr7 128846348 128846536 + CGTGCTGGCCCCAATCGGCCTGGTGCTCATCGTGGGAGGCTACTTCCTCATCCGAGGTGAGTGAAGACCAGGCCAGGACCAGTTGGGCAACAAAATATACTGGGCACTTGCTGCCAGTACTGGGAGCTGCCAGCACG Homo sapiens hg19 +SMO4.chr7.128850341.128850341_tile_1 SMO4.chr7.128850341.128850341_tile_1 1 chr7 128850311 128850499 + GCACCTGGGTCTGGACCAAGGCCACGCTGCTCATCTGGAGGCGTACCTGGTGCAGGTGGGCATGGCAGCCAGCCCCTCCTGCCCTGCCCGCCTCACCCTCAGCCTTGGGACCCCATCTTTAGGTTTTGTCGGGTCCTG Homo sapiens hg19 +SMO5.chr7.128851593.128851593_tile_1 SMO5.chr7.128851593.128851593_tile_1 1 chr7 128851563 128851734 + GTCACCCCTGTGGCAACTCCAGGTATGAGAGTTCAAGCTTCTGGAGGAAGGTGGGGGGAGCACAGAGGCTGGGGGCTTCTGGGACTGGAGTACAGGGGCTGTCGGAGGAGGAGGAAGAG Homo sapiens hg19 +BRAF1.chr7.140453121.140453193_tile_1 BRAF1.chr7.140453121.140453193_tile_1 1 chr7 140453093 140453267 + CACTCCATCGAGATTTCACTGTAGCTAGACCAAAATCACCTATTTTTACTGTGAGGTCTTCATGAAGAAATATATCTGAGGTGTAGTAAGTAAAGGAAAACAGTAGATCTCATTTTCCTATC Homo sapiens hg19 +BRAF28.chr7.140481397.140481478_tile_1 BRAF28.chr7.140481397.140481478_tile_1 1 chr7 140481369 140481545 + ACTGTTCCAAATGATCCAGATCCAATTCTTTGTCCCACTGTAATCTGCCCATCAGGAATCTCCCAATCATCACTCGAGTCCCGTCTACCAAGTGTTTTCTTGATAAAAACAGTAAAAAAGTCA Homo sapiens hg19 +FGFR1_1.chr8.38282209.38282209_tile_1 FGFR1_1.chr8.38282209.38282209_tile_1 1 chr8 38282183 38282360 + GGGGACCGCTCTGTGGAAGATGGGAGAGGAGGCACTTGTCATGGGGACCTTGCCATGGCTAAAGAGGGGTGGGCTCACCTGCGCCCCACTTGGCTTTCCCAGTGATGGGTTGTAAACCTCCCAGCAC Homo sapiens hg19 +FGFR1_2.chr8.38285938.38285938_tile_1 FGFR1_2.chr8.38285938.38285938_tile_1 1 chr8 38285908 38286090 + TCCGAGGAGGGGAGAGCATCTATGGGAAGAAGAAGGGGCACTGAGGTTCCTCCTAGGGACCCCTAGATTTCACCAAGGCTAGTGCAGTTCCAGATGAACACGGACACCCTCCCCATGGGGATCCCAGTC Homo sapiens hg19 +JAK2_1.chr9.5073769.5073770_tile_1 JAK2_1.chr9.5073769.5073770_tile_1 1 chr9 5073737 5073923 + TATGTGTCTGTGGAGACGAGAGTAAGTAAAACTACAGGCTTTCTAATGCCTTTCTCAGAGCATCTGTTTTTGTTTATATAGAAAATTCAGTTTCAGGATCACAGCTAGGTGTCAGTGTAAACTATAATTT Homo sapiens hg19 +CDKN2A1.chr9.21971153.21971187_tile_1 CDKN2A1.chr9.21971153.21971187_tile_1 1 chr9 21971123 21971308 + GGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCC Homo sapiens hg19 +ABL1_1.chr9.133738330.133738364_tile_1 ABL1_1.chr9.133738330.133738364_tile_1 1 chr9 133738302 133738491 + CCATGAAGCACAAGCTGGGCGGGGGCCAGTACGGGGAGGTGTACGAGGGCGTGTGGAAGAAATACAGCCTGACGGTGGCCGTGAAGACCTTGAAGGTAGGCTGGGACTGCCGGGGGTGCCCAGGGTACGTGGGGCAAG Homo sapiens hg19 +ABL1_9.chr9.133747520.133747520_tile_1 ABL1_9.chr9.133747520.133747520_tile_1 1 chr9 133747476 133747664 + TTTCCTTCTGCAGGAGGACACCATGGAGGTGGAAGAGTTCTTGAAAGAAGCTGCAGTCATGAAAGAGATCAAACACCCTAACCTGGTGCAGCTCCTTGGTGAGTAAGCCCGGGGCTCTGAAGAGAGGGTCTCGCGCCGC Homo sapiens hg19 +ABL1_10.chr9.133748283.133748414_tile_1 ABL1_10.chr9.133748283.133748414_tile_1 1 chr9 133748157 133748327 - CCCGTAGGTCATGAACTCAGTGATGATATAGAACGGGGGCTCCCGGGTGCAGACCCCTGCCAACAAGACAACGAGGACTTCAACACGTGGCTCCGCTCCCAACTGAACAAACAACT Homo sapiens hg19 +ABL1_10.chr9.133748283.133748414_tile_2 ABL1_10.chr9.133748283.133748414_tile_2 1 chr9 133748277 133748457 + GAACCTCCTGGACTACCTGAGGGAGTGCAACCGGCAGGAGGTGAACGCCGTGGTGCTGCTGTACATGGCCACTCAGATCTCGTCAGCCATGGAGTACCTGGAGAAGAAAAACTTCATCCACAGGTAGGGGCCT Homo sapiens hg19 +ABL1_16.chr9.133750356.133750356_tile_1 ABL1_16.chr9.133750356.133750356_tile_1 1 chr9 133750328 133750516 + GCCCATGCTGGAGCCAAGTTCCCCATCAAATGGACTGCACCCGAGAGCCTGGCCTACAACAAGTTCTCCATCAAGTCCGACGTCTGGGGTAAGGGCTGCTGCTGCACTGAAGTGGTCCTTCCTGACTACAGGAGGGTT Homo sapiens hg19 +NOTCH1_1.chr9.139397768.139397768_tile_1 NOTCH1_1.chr9.139397768.139397768_tile_1 1 chr9 139397740 139397928 + CCAGGTAGACGATGGAGCTGGGCGGACAATCAGAGAGGGGCTGGGACCCGAGGCTTCCTCCTCCCCCGCCCACCGGCCAGGGATGCTGCCGCAGGACACTGAGGCCCATGACGCCACAGTCAGGACATGGTGAGGC Homo sapiens hg19 +NOTCH1_2.chr9.139399344.139399422_tile_1 NOTCH1_2.chr9.139399344.139399422_tile_1 1 chr9 139399316 139399485 + GCAGCACGCGGCTGAGCTCCCGCAGGAAGTGGAAGGAGCTGTTGCGCAGCTGCTCCGGCGGCATCAGCACCACCACCACCAGCGTGCCGGCCGCCAGCCTCTCGGGTACATGCTCCGC Homo sapiens hg19 +RET1.chr10.43609078.43609104_tile_1 RET1.chr10.43609078.43609104_tile_1 1 chr10 43609048 43609226 + CTGCTTCCCTGAGGAGGAGAAGTGCTTCTGCGAGCCCGAAGACATCCAGGGTGAGTGGGTGGCGGCCGGGACCACCACCACCTCCCAGCCCCACAGAGGTCTCAACAGCACATCTGAGGTCCCAACAA Homo sapiens hg19 +RET2_9.chr10.43609940.43609950_tile_1 RET2_9.chr10.43609940.43609950_tile_1 1 chr10 43609902 43610075 - TGGCTTGTGGGCAAACTTGTGGTAGCAGTGGATGCAGAAGGCAGACAGCAGCACCGAGACGATGAAGGAGAAGAGGACAGCGGCTGCGATCACCGTGCGGCACAGCTCGTCGCACAGTGG Homo sapiens hg19 +RET10.chr10.43613840.43613840_tile_1 RET10.chr10.43613840.43613840_tile_1 1 chr10 43613810 43613998 + CGAGTGAGCTGCGAGACCTGCTGTCAGAGTTCAACGTCCTGAAGCAGGTCAACCACCCACATGTCATCAAATTGTATGGGGCCTGCAGCCAGGATGGTAAGGCCAGCTGCAGGGTGAGGTGGGCAGCCACTGCACCCAG Homo sapiens hg19 +RET11_12.chr10.43615567.43615569_tile_1 RET11_12.chr10.43615567.43615569_tile_1 1 chr10 43615533 43615703 + CCTGGTAGCTGAGGGGCGGAAGATGAAGATTTCGGATTTCGGCTTGTCCCGAGATGTTTATGAAGAGGATTCCTACGTGAAGAGGAGCCAGGTGCCCAGTCCCGGGGATGAGGCGGGG Homo sapiens hg19 +RET13.chr10.43617416.43617416_tile_1 RET13.chr10.43617416.43617416_tile_1 1 chr10 43617388 43617564 + ATGGCAATTGAATCCCTTTTTGATCATATCTACACCACGCAAAGTGATGTGTAAGTGTGGGTGTTGCTCTCTTGGGGTGGAGGTTACAGAAACACCCTTATACATGTAGTGGGGCCACGACGC Homo sapiens hg19 +PTEN1.chr10.89624242.89624244_tile_1 PTEN1.chr10.89624242.89624244_tile_1 1 chr10 89624214 89624388 + CAAAGAGATCGTTAGCAGAAACAAAAGGAGATATCAAGAGGATGGATTCGACTTAGACTTGACCTGTATCCATTTCTGCGGCTGCTCCTCTTTACCTTTCTGTCACTCTCTTAGAACGTGG Homo sapiens hg19 +PTEN3.chr10.89685307.89685307_tile_1 PTEN3.chr10.89685307.89685307_tile_1 1 chr10 89685275 89685459 + ATATACAATCTGTAAGTATGTTTTCTTATTTGTATGCTTGCAAATATCTTCTAAAACAACTATTAAGTGAAAGTTATCTGCTTGTTAGAGTGAGGTAGAGTTAAAGATACATTTTAACAGAATTGTATT Homo sapiens hg19 +PTEN4.chr10.89711893.89711900_tile_1 PTEN4.chr10.89711893.89711900_tile_1 1 chr10 89711865 89712039 + GTCAGAGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCATCTGGATTATAGACCAGTGGCACTGTTGTTTCACAAGATGATGTTTGAAACTATTCCAATGTTCAGTGGCGGAACT Homo sapiens hg19 +PTEN7.chr10.89717615.89717772_tile_1 PTEN7.chr10.89717615.89717772_tile_1 1 chr10 89717489 89717668 + ATATTGCTGATATTAATCATTAAAATCGTTTTTGACAGTTTGACAGTTAAAGGCATTTCCTGTGAAATAATACTGGTATGTATTTAACCATGCAGATCCTCAGTTTGTGGTCTGCCAGCTAAAG Homo sapiens hg19 +PTEN7.chr10.89717615.89717772_tile_2 PTEN7.chr10.89717615.89717772_tile_2 1 chr10 89717615 89717801 - TTTAGCATCTTGTTCTGTTTGTGGAAGAACTCTACTTTGATATCACCACACACAGGTAACGGCTGAGGGAACTCAAAGTACATGAACTTGTCTTCCCGTCGTGTGGGTCCTGAATTGGAGGAATATATCTTCACC Homo sapiens hg19 +PTEN13.chr10.89720716.89720852_tile_1 PTEN13.chr10.89720716.89720852_tile_1 1 chr10 89720684 89720870 + CAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATCGATAGCATTTGCAGTATAGAGCGTGCAGATAATGACAAGGAATATCTAGTACTTACTTTAACAAAAAATGATCTTGACAAAGCAAATAAAGACA Homo sapiens hg19 +PTEN13.chr10.89720716.89720852_tile_2 PTEN13.chr10.89720716.89720852_tile_2 1 chr10 89720814 89720991 - TTCTTCATCAGCTGTACTCCTAGAATTAAACACACATCACATACATACAAGTCAACAACCCCCACAAAATGTTTAATTTAACTGACCTTAAAATTTGGAGAAAAGTATCGGTTGGCTTT Homo sapiens hg19 +FGFR2_1.chr10.123258034.123258034_tile_1 FGFR2_1.chr10.123258034.123258034_tile_1 1 chr10 123258006 123258184 + GATTTATGATATTCTTGTGTTTCCCAATCATCTTCATCATCTCCATCTCTGACACCAGATCAGAAAGGTCTTTCTCTGTGGCATCATCTATGAACAGTAGGCATATTCACAAATCAGTTCATTTC Homo sapiens hg19 +FGFR2_2.chr10.123274774.123274803_tile_1 FGFR2_2.chr10.123274774.123274803_tile_1 1 chr10 123274746 123274930 + CAGTAAATGGCTATCTCCAGGTAGTCTGGGGAAGCTGTAATCTCCTTTTCTCTTCCAGGCGCTAGATTGCAGATCACAGGAGGAGGAACAGATAAGCAGGCCATAGAGTTAGCACACCAGACTGACGCATC Homo sapiens hg19 +FGFR2_5.chr10.123279503.123279677_tile_1 FGFR2_5.chr10.123279503.123279677_tile_1 1 chr10 123279385 123279555 + AACAGGAAATCAAAGAACCTGTGGCCAAACCCATGAAGGAGACCCCAGTTGTGGGTACCTTTAGATTCAGAAAGTCCTCACCTTGAGAACCTTGAGGTAGGGCAGCCCGTCGGGCCC Homo sapiens hg19 +FGFR2_5.chr10.123279503.123279677_tile_2 FGFR2_5.chr10.123279503.123279677_tile_2 1 chr10 123279471 123279640 - ACGTAGAGTTTGTCTGCAAGGTTTACAGTGATGCCCAGCCCCACATCCAGTGGATCAAGCACGTGGAAAAGAACGGCAGTAAATACGGGCCCGACGGGCTGCCCTACCTCAAGGTT Homo sapiens hg19 +FGFR2_5.chr10.123279503.123279677_tile_3 FGFR2_5.chr10.123279503.123279677_tile_3 1 chr10 123279587 123279769 + TCTCCTCCGACCACTGTGGAGGCATTTGCCGGCAGTCCGGCTTGGAGGATGGGCCGGTGAGGCGATCGCTCTGGTGGAGAGAGGGAAGAAAGGAGGAGTGGGGATGGGAGAATGAGAGACCAATAAATA Homo sapiens hg19 +HRAS1.chr11.533873.533875_tile_1 HRAS1.chr11.533873.533875_tile_1 1 chr11 533843 534021 + CCTCCTGGCCGGCGGTATCCAGGATGTCCAACAGGCACGTCTCCCCATCAATGACCACCTGCTTCCGGTAGGAATCCTGCAGGAGGACAGGGCTCAGGGACCCCCTCAGGACCTTCCGTGGGGGGA Homo sapiens hg19 +HRAS6.chr11.534285.534289_tile_1 HRAS6.chr11.534285.534289_tile_1 1 chr11 534251 534434 + GCCCACACCGCCGGCGCCCACCACCACCAGCTTATATTCCGTCATCGCTCCTCAGGGGCCTGCGGCCCGGGGTCCTCCTACAGGGTCTCCTGCCCCACCTGCCAAGGAGGGCCCTGCTCAGCCAGGCCCAGGC Homo sapiens hg19 +ATM1.chr11.108117847.108117848_tile_1 ATM1.chr11.108117847.108117848_tile_1 1 chr11 108117817 108117989 + TGTCACCAGGTACAGTAAGTAGGTCATGTCACATTTAGAAATTTCCTGTTAATTTTTTTTTTAAACTGGGCATTTTGGGCTTTTAAAACCTGTGTTCTCACAAAAAGCCTATAAAAT Homo sapiens hg19 +ATM2.chr11.108119823.108119823_tile_1 ATM2.chr11.108119823.108119823_tile_1 1 chr11 108119793 108119963 + TTGTGCCTTGGTAAAGTGTTACCATTTTCTCATTCAGTGTCATTTTAATCTCTTGTATGTTATTTTTCAGAAAACTTTCAGTGGAATCCTTTCATCTCAACCAGAACTAAGTCATTT Homo sapiens hg19 +ATM3.chr11.108123551.108123551_tile_1 ATM3.chr11.108123551.108123551_tile_1 1 chr11 108123513 108123683 + AGTAATTTTCCTCATCTTGTACTGGAGAAAATTCTTGTGAGTCTCACTATGAAAAACTGTAAAGCTGCAATGAATTTTTTCCAAAGCGTGCCAGAATGGTATGTTATCTAATA Homo sapiens hg19 +ATM4.chr11.108137973.108138003_tile_1 ATM4.chr11.108137973.108138003_tile_1 1 chr11 108137939 108138126 + TAATGGAGGTGGAGGATCAGTCATCCATGAATCTATTTAACGATTACCCTGATAGTAGTGTTAGTGATGCAAACGAACCTGGAGAGAGCCAAAGTACCATAGGTAAATACATATTTACTACTTGGGATT Homo sapiens hg19 +ATM6.chr11.108155132.108155132_tile_1 ATM6.chr11.108155132.108155132_tile_1 1 chr11 108155104 108155281 + GGCACAGCAAAGAGAGACTGCTACCAAGGTCTATGATATGCTTAAAAGTGAAAACTTATTGGGAAAACAGGTATGGCTTCAATTTTTATGTACTTTTCATTCCCTGAATGATATGAGATAT Homo sapiens hg19 +ATM7.chr11.108170476.108170479_tile_1 ATM7.chr11.108170476.108170479_tile_1 1 chr11 108170442 108170618 + GGGTCCTATAGATTTCTCTACCATAGCTATACAACATAGTAAAGATGCATCTTATACCAAGGCCCTTAAGTTATTTGAAGATAAAGAACTTCAGTGGACCTTCATAATGCTGACCTACCTGAA Homo sapiens hg19 +ATM9.chr11.108172421.108172421_tile_1 ATM9.chr11.108172421.108172421_tile_1 1 chr11 108172391 108172571 + TTAGCCACAAAGACTGGACATAGTTTCTGGGAGATTTATAAGATGACAACAGATCCAATGCTGGCCTATCTACAGCCTTTTAGAACATCAAGAAAAAAGGTCTCTTAAGTAATAAATGTTTATTGAA Homo sapiens hg19 +ATM10.chr11.108173640.108173640_tile_1 ATM10.chr11.108173640.108173640_tile_1 1 chr11 108173612 108173801 + AAATCTGTGGATTCCTCTAAGTGAAAATCATGACATTTGGATAAAGACACTGACTTGTGCTTTTTTGGACAGTGGAGGCACAAAATGTGAAATTCTTCAATTATTAAAGCCAATGTGTGAAGTAAGAAGATTAATT Homo sapiens hg19 +ATM11.chr11.108180945.108180945_tile_1 ATM11.chr11.108180945.108180945_tile_1 1 chr11 108180915 108181101 + AAGTTGCCAAGGTAGCTCAGTCTTGTGCTGCTCACTTTACAGCTTTACTCTATGCAGAAATCTATGCAGATAAGAAAAGTATGGATGATCAAGAGAAAAGGTAATGGAATTTAGAATTTTTGGTTTTTAAAA Homo sapiens hg19 +ATM12.chr11.108200958.108200961_tile_1 ATM12.chr11.108200958.108200961_tile_1 1 chr11 108200926 108201096 + TTCAGCGAGAGCTGGAGTTGGATGAATTAGCCCTGCGTGCACTGAAAGAGGATCGTAAACGCTTCTTATGTAAAGCAGTTGAAAATTATATCAACTGCTTATTAAGTGGAGAAGA Homo sapiens hg19 +ATM14.chr11.108204681.108204681_tile_1 ATM14.chr11.108204681.108204681_tile_1 1 chr11 108204651 108204823 + TACTATGGAAATTAAGGTAATTTGCAATTAACTCTTGATTTTTTTTAAACTAAATTTTTTTTATTAGATTGAACCATTTGAAATAGTATTTTTATGTAGGTCAAAATTGGTTAAATA Homo sapiens hg19 +ATM15.chr11.108205769.108205769_tile_1 ATM15.chr11.108205769.108205769_tile_1 1 chr11 108205739 108205928 + AGGTGTAAATTTACCAAAAATAATAGATTGTGTAGGTTCCGATGGCAAGGAGAGGAGACAGCTTGTTAAGGTGAGCCTTCCCTTCTCTGGCTTAGCCCTTAGAGTTTTAGTGATGAAAATTTTTAGTTCATATT Homo sapiens hg19 +ATM16.chr11.108206594.108206594_tile_1 ATM16.chr11.108206594.108206594_tile_1 1 chr11 108206566 108206750 + GATGCTGTCATGCAACAGGTCTTCCAGATGTGTAATACATTACTGCAGAGAAACACGGAAACTAGGAAGAGGAAATTAACTATCTGTACTTATAAGGTAACTATTTGTACTTCTGTTAGTTCACCAAAAAC Homo sapiens hg19 +ATM17.chr11.108218089.108218089_tile_1 ATM17.chr11.108218089.108218089_tile_1 1 chr11 108218061 108218247 + TCTAGGTAAGTAATAAAATCTATGTATCTATTCTTTTTAGTAAATATTTGGTCATCATGGAATGTTGTTTGCCTACCAAGATATTACAAATATAAGAGACAGATAAATTGAAGCAGTAAATATTGGGTTTTTT Homo sapiens hg19 +ATM18.chr11.108225590.108225590_tile_1 ATM18.chr11.108225590.108225590_tile_1 1 chr11 108225562 108225751 + AACCATTGTAGAGGTAAAGTATTTTATAAGGAAGACTTTATTTTTTTTCTTACCAGGTAGACTGTGTATCTCATCAGGAAGTCACTGATGTGAAGAGCACTGCTTCATTTTAACATAGGGGGATGTGGCTGGGCAGC Homo sapiens hg19 +ATM19.chr11.108236086.108236203_tile_1 ATM19.chr11.108236086.108236203_tile_1 1 chr11 108236058 108236241 + ACGTGTCTTAATGAGACTACAAGAGAAACTGAAAGGAGTGGAAGAAGGCACTGTGCTCAGTGTTGGTGGACAAGTGAATTTGCTCATACAGCAGGCCATAGACCCCAAAAATCTCAGCCGACTTTTCCCAG Homo sapiens hg19 +KRAS1.chr12.25378562.25378562_tile_1 KRAS1.chr12.25378562.25378562_tile_1 1 chr12 25378532 25378717 + TTGCTGATGTTTCAATAAAAGGAATTCCATAACTTCTTGCTAAGTCCTGAGCCTGTTTTGTGTCTACTGTTCTAGAAGGCAAATCACATTTATTTCCTACTAGGACCATAGGTACATCTTCAGAGTCCTTA Homo sapiens hg19 +KRAS2.chr12.25380275.25380283_tile_1 KRAS2.chr12.25380275.25380283_tile_1 1 chr12 25380245 25380427 + CCTCTTGACCTGCTGTGTCGAGAATATCCAAGAGACAGGTTTCTCCATCAATTACTACTTGCTTCCTGTAGGAATCCTGAGAAGGGAGAAACACAGTCTGGATTATTACAGTGCACCTTTTACTTCAA Homo sapiens hg19 +KRAS7.chr12.25398255.25398285_tile_1 KRAS7.chr12.25398255.25398285_tile_1 1 chr12 25398225 25398414 + TGTATCGTCAAGGCACTCTTGCCTACGCCACCAGCTCCAACTACCACAAGTTTATATTCAGTCATTTTCAGCAGGCCTTATAATAAAAATAATGAAAATGTGACTATATTAGAACATGTCACACATAAGGTTA Homo sapiens hg19 +PTPN11_1.chr12.112888163.112888211_tile_1 PTPN11_1.chr12.112888163.112888211_tile_1 1 chr12 112888135 112888323 + TGGTGATTACTATGACCTGTATGGAGGGGAGAAATTTGCCACTTTGGCTGAGTTGGTCCAGTATTACATGGAACATCACGGGCAATTAAAAGAGAAGAATGGAGATGTCATTGAGCTTAAATATCCTCTGAACTGT Homo sapiens hg19 +PTPN11_10.chr12.112926884.112926888_tile_1 PTPN11_10.chr12.112926884.112926888_tile_1 1 chr12 112926856 112927032 + GGTCAGGGATGGTCCAGACAGAAGCACAGTACCGATTTATCTATATGGCGGTCCAGCATTATATTGAAACACTACAGCGCAGGATTGAAGAAGAGCAGGTACCAGCCTGAGGGCTGGCATGCGG Homo sapiens hg19 +HNF1A_1.chr12.121431413.121431414_tile_1 HNF1A_1.chr12.121431413.121431414_tile_1 1 chr12 121431385 121431558 + GTGGGGCCCAGCATCCCAGCAGATCCTGTTCCAGGCCTATGAGAGGCAGAAGAACCCTAGCAAGGAGGAGCGAGAGACGCTAGTGGAGGAGTGCAATAGGTACAACGGCGGGCGGGAAACAG Homo sapiens hg19 +HNF1A_3.chr12.121432070.121432070_tile_1 HNF1A_3.chr12.121432070.121432070_tile_1 1 chr12 121432042 121432221 + GCGCAAAGAAGAAGCCTTCCGGCACAAGCTGGCCATGGACACGTACAGCGGGCCCCCCCCAGGGCCAGGCCCGGGACCTGCGCTGCCCGCTCACAGCTCCCCTGGCCTGCCTCCACCTGCCCTCTCCCCC Homo sapiens hg19 +FLT3_1.chr13.28592620.28592653_tile_1 FLT3_1.chr13.28592620.28592653_tile_1 1 chr13 28592590 28592766 + CATAGTTGGAATCACTCATGATATCTCGAGCCAATCCAAAGTCACATATCTTCACCACTTTCCCGTGGGTGACAAGCACGTTCCTGGCGGCCAGGTCTCTGTGAACACACTGTCAAGAATGA Homo sapiens hg19 +FLT3_13.chr13.28602329.28602329_tile_1 FLT3_13.chr13.28602329.28602329_tile_1 1 chr13 28602295 28602464 + GTGTGCACGCCCCCAGCAGGTTCACAATATTCTCGTGGCTTCCCAGCTGGGTCATCATCTTGAGTTCTGACATGAGTGCCTCTCTTTCAGAGCTGTCTGCTTTTTCTGTCAAAGAA Homo sapiens hg19 +FLT3_14.chr13.28608244.28608341_tile_1 FLT3_14.chr13.28608244.28608341_tile_1 1 chr13 28608214 28608402 + ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATCTGTAGCTGGCTTTCATACCTAAATTGCTTCAGAGATGAAATGATGAGTCA Homo sapiens hg19 +FLT3_22.chr13.28610138.28610138_tile_1 FLT3_22.chr13.28610138.28610138_tile_1 1 chr13 28610098 28610267 - TATAGGAGTGAACCACTATGCCCAGCCAGTGAGCTTATTTCACACGTTCTTTTCTATAGGGAAACCTCAAGTGCTCGCAGAAGCATCGGCAAGTCAGGCGTCCTGTTTCTCGGATGG Homo sapiens hg19 +RB1_1.chr13.48919244.48919244_tile_1 RB1_1.chr13.48919244.48919244_tile_1 1 chr13 48919156 48919336 + ATTTACTTTTTTCTATTCTTTCCTTTGTAGTGTCCATAAATTCTTTAACTTACTAAAAGAAATTGATACCAGTACCAAAGTTGATAATGCTATGTCAAGACTGTTGAAGAAGTATGATGTATTG Homo sapiens hg19 +RB1_2.chr13.48923148.48923148_tile_1 RB1_2.chr13.48923148.48923148_tile_1 1 chr13 48923120 48923296 + TTATTAGCTAAAGGTAAGTTCATTATATTTATTAAATGCTAATATTTCAAATGTAATAATTAAATTGGCATTCCTTTGGACTAAATTCCCCAATTTTTATTGAGTAATGTACTCCTCCCTCAT Homo sapiens hg19 +RB1_3.chr13.48942685.48942685_tile_1 RB1_3.chr13.48942685.48942685_tile_1 1 chr13 48942655 48942826 + ACGAAAAAGTAACCTTGATGAAGAGGTGAATGTAATTCCTCCACACACTCCAGTTAGGTATGAATTTTCCTACTTTTAATTATATTATAATTTTGTTATTCATGGCTTTATAGTG Homo sapiens hg19 +RB1_4.chr13.48955538.48955550_tile_1 RB1_4.chr13.48955538.48955550_tile_1 1 chr13 48955504 48955684 + TAGAACGATGTGAACATCGAATCATGGAATCCCTTGCATGGCTCTCAGTAAGTAGCTAAATAATTGAAGAAATTCATTCATGTGCATATGGCTAACAAATTATTGTTAGTGAGAGGTGTTTCTTA Homo sapiens hg19 +RB1_6.chr13.49027168.49027168_tile_1 RB1_6.chr13.49027168.49027168_tile_1 1 chr13 49027112 49027288 + TTTGATCTTATTAAACAATCAAAGGACCGAGAAGGACCAACTGATCACCTTGAATCTGCTTGTCCTCTTAATCTTCCTCTCCAGAATAATCACACTGCAGCAGATATGTAAGCAAAATATA Homo sapiens hg19 +RB1_7.chr13.49033843.49033846_tile_1 RB1_7.chr13.49033843.49033846_tile_1 1 chr13 49033813 49033989 + TCTCCGGCTAAATACACTTTGTGAACGCCTTCTGTCTGAGCACCCAGAATTAGAACATATCATCTGGACCCTTTTCCAGCACACCCTGCAGAATGAGTATGAACTCATGAGAGACAGGCATTT Homo sapiens hg19 +RB1_8.chr13.49037877.49037877_tile_1 RB1_8.chr13.49037877.49037877_tile_1 1 chr13 49037815 49037985 + TTTACATCAATTTATTTACTAGATTATGATGTGTTCCATGTATGGCATATGCAAAGTGAAGAATATAGACCTTAAATTCAAAATCATTGTAACAGCATACAAGGATCTTCCTCA Homo sapiens hg19 +RB1_9.chr13.49039164.49039164_tile_1 RB1_9.chr13.49039164.49039164_tile_1 1 chr13 49039132 49039304 + AAGAGGAGTATGATTCTATTATAGTATTCTATAACTCGGTCTTCATGCAGAGACTGAAAACAAATATTTTGCAGTATGCTTCCACCAGGGTAGGTCAAAAGTATCCTTTGATTGGAAAA Homo sapiens hg19 +AKT1.chr14.105246455.105246455_tile_1 AKT1.chr14.105246455.105246455_tile_1 1 chr14 105246429 105246600 + CTCACGTTGGTCCACATCCTGCGGCCGCTCCTTGTAGCCAATGAAGGTGCCATCATTCTTGAGGAGGAAGTAGCGTGGCCGCCAGGTCTTGATGTACTCCCCTACAGACGTGCGGGTGGTGA Homo sapiens hg19 +CDH1_1.chr16.68835649.68835650_tile_1 CDH1_1.chr16.68835649.68835650_tile_1 1 chr16 68835613 68835782 + TGGGCACAGATGGTGTGATTACAGTCAAAAGGCCTCTACGGTTTCATAACCCACAGATCCATTTCTTGGTCTACGCCTGGGACTCCACCTACAGAAAGTTTTCCACCAAAGTCACGCTGAAT Homo sapiens hg19 +CDH1_2.chr16.68846137.68846137_tile_1 CDH1_2.chr16.68846137.68846137_tile_1 1 chr16 68846109 68846283 + CGATAATCCTCCGATCTTCAATCCCACCACGGTAATTCTATAACTCCTTAGAGGGTTTCCAAAGAAAGGTCTTTTGTTGTTCATGAACTAAGTGTCACCACTGCTCATGGGCGAAGTCTTT Homo sapiens hg19 +CDH1_3.chr16.68847274.68847277_tile_1 CDH1_3.chr16.68847274.68847277_tile_1 1 chr16 68847246 68847422 + ACTGATGCTGATGCCCCCAATACCCCAGCGTGGGAGGCTGTATACACCATATTGAATGATGATGGTGGACAATTTGTCGTCACCACAAATCCAGTGAACAACGATGGCATTTTGAAAACAGCA Homo sapiens hg19 +TP53_1.chr17.7574003.7574021_tile_1 TP53_1.chr17.7574003.7574021_tile_1 1 chr17 7573977 7574147 + CGGAACATCTCGAAGCGCTCACGCCCACGGATCTGCAGCAACAGAGGAGGGGGAGAAGTAAGTATATACACAGTACCTGAGTTAAAAGATGGTTCAAGTTACAATTGTTTGACTTTATG Homo sapiens hg19 +TP53_3.chr17.7577022.7577129_tile_1 TP53_3.chr17.7577022.7577129_tile_1 1 chr17 7576996 7577166 + CGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCG Homo sapiens hg19 +TP53_17.chr17.7577523.7577574_tile_1 TP53_17.chr17.7577523.7577574_tile_1 1 chr17 7577495 7577683 + GGTGAGGATGGGCCTCCGGTTCATGCCGCCCATGCAGGAACTGTTACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAACCTAGGAGATAACACAGGCCCAAGATGAGGCCAGTGCGCCTTGGGGAGA Homo sapiens hg19 +TP53_31_59.chr17.7578190.7578536_tile_1 TP53_31_59.chr17.7578190.7578536_tile_1 1 chr17 7578064 7578234 + AGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTA Homo sapiens hg19 +TP53_31_59.chr17.7578190.7578536_tile_2 TP53_31_59.chr17.7578190.7578536_tile_2 1 chr17 7578156 7578325 - CTGATTGCTCTTAGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCGACATAGTGTGGTGGTGCCCTATGAGCCGCC Homo sapiens hg19 +TP53_31_59.chr17.7578190.7578536_tile_3 TP53_31_59.chr17.7578190.7578536_tile_3 1 chr17 7578246 7578415 + TGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCG Homo sapiens hg19 +TP53_31_59.chr17.7578190.7578536_tile_4 TP53_31_59.chr17.7578190.7578536_tile_4 1 chr17 7578346 7578515 - GTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCG Homo sapiens hg19 +TP53_31_59.chr17.7578190.7578536_tile_5 TP53_31_59.chr17.7578190.7578536_tile_5 1 chr17 7578468 7578645 + CCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGA Homo sapiens hg19 +TP53_60.chr17.7579358.7579403_tile_1 TP53_60.chr17.7579358.7579403_tile_1 1 chr17 7579324 7579507 + GCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAG Homo sapiens hg19 +TP53_64.chr17.7579882.7579882_tile_1 TP53_64.chr17.7579882.7579882_tile_1 1 chr17 7579852 7580032 + GCTCGACGCTAGGATCTGACTGCGGCTCCTCCATGGCAGTGACCCGGAAGGCAGTCTGGCTGCTGCAAGAGGAAAAGTGGGGATCCAGCATGAGACACTTCCAACCCTGGGTCACCTGGGCCTGCAG Homo sapiens hg19 +ERBB2_1.chr17.37880219.37880261_tile_1 ERBB2_1.chr17.37880219.37880261_tile_1 1 chr17 37880191 37880361 + TGTTGAGGGAAAACACATCCCCCAAAGCCAACAAAGAAATCTTAGACGTAAGCCCCTCCACCCTCTCCTGCTAGGAGGACAGGAAGGACCCCATGGCTGCAGGTCTGGGCTCTGGTCT Homo sapiens hg19 +ERBB2_4.chr17.37880993.37881012_tile_1 ERBB2_4.chr17.37880993.37881012_tile_1 1 chr17 37880963 37881151 + CGTGATGGCTGGTGTGGGCTCCCCATATGTCTCCCGCCTTCTGGGCATCTGCCTGACATCCACGGTGCAGCTGGTGACACAGCTTATGCCCTATGGCTGCCTCTTAGACCATGTCCGGGAAAACCGCGGACGCCTGGG Homo sapiens hg19 +ERBB2_13.chr17.37881332.37881440_tile_1 ERBB2_13.chr17.37881332.37881440_tile_1 1 chr17 37881298 37881482 + GCGGCTCGTACACAGGGACTTGGCCGCTCGGAACGTGCTGGTCAAGAGTCCCAACCATGTCAAAATTACAGACTTCGGGCTGGCTCGGCTGCTGGACATTGACGAGACAGAGTACCATGCAGATGGGGGCA Homo sapiens hg19 +SMAD4_1.chr18.48575169.48575170_tile_1 SMAD4_1.chr18.48575169.48575170_tile_1 1 chr18 48575131 48575301 + TTTGACTTAAAATGTGATAGTGTCTGTGTGAATCCATATCACTACGAACGAGTTGTATCACCTGGAATTGGTAAGTAGACTTTGCTTTCATCCTAAGAAACATAAAGGGAAA Homo sapiens hg19 +SMAD4_2.chr18.48581198.48581198_tile_1 SMAD4_2.chr18.48581198.48581198_tile_1 1 chr18 48581168 48581346 + AGGGACAGCCATCGTTGTCCACTGAAGGACATTCAATTCAAACCATCCAGCATCCACCAAGTAATCGTGCATCGACAGAGACATACAGCACCCCAGCTCTGTTAGCCCCATCTGAGTCTAATGC Homo sapiens hg19 +SMAD4_3.chr18.48584560.48584560_tile_1 SMAD4_3.chr18.48584560.48584560_tile_1 1 chr18 48584528 48584714 + GGGCCTCAGCCAGGACAGCAGCAGAATGGATTTACTGGTCAGCCAGCTACTTACCATCATAGTATGTACATACTTTAAAAAATCTTTTAAATAGTTGAGAAAAAAGTAGGCAGCCTTTATAAAAGCAAATTAAC Homo sapiens hg19 +SMAD4_4.chr18.48586262.48586262_tile_1 SMAD4_4.chr18.48586262.48586262_tile_1 1 chr18 48586234 48586416 + CCAGCCTCCCATTTCCAATCATCCTGGTAAGTGTATTTCAAAATTGATTTCCTGTATTTAGATTGATTTAGTGGTGATTGAAACGCACAAACACAGGCTTTAATGGAATTATGGGGTCACTTCTCAGAT Homo sapiens hg19 +SMAD4_5.chr18.48591826.48591919_tile_1 SMAD4_5.chr18.48591826.48591919_tile_1 1 chr18 48591796 48591982 + TTGAAATGGATGTTCAGGTAGGAGAGACATTTAAGGTTCCTTCAAGCTGCCCTATTGTTACTGTTGATGGATACGTGGACCCTTCTGGAGGAGATCGCTTTTGTTTGGGTCAACTCTCCAATGTCCACAGGAC Homo sapiens hg19 +SMAD4_11.chr18.48593405.48593405_tile_1 SMAD4_11.chr18.48593405.48593405_tile_1 1 chr18 48593377 48593547 + AAGGTGTGCAGTTGGAATGTAAAGGTGAAGGTGATGTTTGGGTCAGGTGCCTTAGTGACCACGCGGTCTTTGTACAGAGTTACTACTTAGACAGAGAAGCTGGGCGTGCACCTGGAGA Homo sapiens hg19 +SMAD4_12.chr18.48603032.48603094_tile_1 SMAD4_12.chr18.48603032.48603094_tile_1 1 chr18 48602998 48603168 + TGTCATCGACAGATGCAGCAGCAGGCGGCTACTGCACAAGCTGCAGCAGCTGCCCAGGCAGCAGCCGTGGCAGGAAACATCCCTGGCCCAGGATCAGTAGGTGGAATAGCTCCA Homo sapiens hg19 +SMAD4_15.chr18.48604668.48604754_tile_1 SMAD4_15.chr18.48604668.48604754_tile_1 1 chr18 48604638 48604808 + CGTCGCTTATGCATACTCAGGATGAGTTTTGTGAAAGGCTGGGGACCGGATTACCCAAGACAGAGCATCAAAGAAACACCTTGCTGGATTGAAATTCACTTACACCGGGCCCTCCAGC Homo sapiens hg19 +STK11_1.chr19.1207021.1207092_tile_1 STK11_1.chr19.1207021.1207092_tile_1 1 chr19 1206993 1207169 + CCAGCCGCGCCGCAAGCGGGCCAAGCTCATCGGCAAGTACCTGATGGGGGACCTGCTGGGGGAAGGCTCTTACGGCAAGGTGAAGGAGGTGCTGGACTCGGAGACGCTGTGCAGGAGGGCCGT Homo sapiens hg19 +STK11_4.chr19.1220487.1220502_tile_1 STK11_4.chr19.1220487.1220502_tile_1 1 chr19 1220459 1220638 + CCGACCTGGGCGTGGCCGAGGTAGGCACGTGCTAGGGGGGGCCCTGGGGCGCCCCCTCCCGGGCACTCCCTGAGGGCTGCACGGCACCGCCACAGGCACTGCACCCGTTCGCGGCGGACGACACCTGCCG Homo sapiens hg19 +STK11_8.chr19.1221264.1221319_tile_1 STK11_8.chr19.1221264.1221319_tile_1 1 chr19 1221232 1221407 - CCCGCCTCCCTGGGGCTGCGGGCAGAGGGATGAGGCTCCCACCTTTCAGCAGGTCAGAGAGCGGGGGGCCACAGTCGCCCGGGATGGCGTAGCTCCCCTTCCCGATGTTCTCAAACAACTTG Homo sapiens hg19 +STK11_12.chr19.1223059.1223125_tile_1 STK11_12.chr19.1223059.1223125_tile_1 1 chr19 1223035 1223221 + GGCGCAGCATGACTGTGGTGCCGTACTTGGAGGACCTGCACGGCGCGGACGAGGACGAGGACCTCTTCGACATCGAGGATGACATCATCTACACTCAGGACTTCACGGTGCCCGGTGAGTCTGGCGGGGGCCCCTGCCC Homo sapiens hg19 +JAK3_1.chr19.17945696.17945696_tile_1 JAK3_1.chr19.17945696.17945696_tile_1 1 chr19 17945666 17945840 + GGTGACGCCACTAAACACTTCCCAGACCGTGGCGCCGAAGCCCCACTTGTCAGCTTCCAAGCTAAGTGTCTGCGCCTCCCGGAGACACTCGGGGGCCACCCAGGGGATCCTGTCGGTGAGCAC Homo sapiens hg19 +JAK3_2.chr19.17948009.17948009_tile_1 JAK3_2.chr19.17948009.17948009_tile_1 1 chr19 17947981 17948169 + CGCTGCTTCCAGGAATGACTGGGGAAGGTGGGAAGGGAGAGAAGATGCGTGGGTTTCTTCCACTCCAATAATCCCAAATTTTGTGCTCACAGACCTGCCTTAGGGGAACACCTGGCCACAGGTCACCTTTGGCCCTGG Homo sapiens hg19 +SRC.chr20.36031762.36031762_tile_1 SRC.chr20.36031762.36031762_tile_1 1 chr20 36031734 36031923 + CCAGCCCGGGGAGAACCTCTAGGCACAGGCGGGCCCAGACCGGCTTCTCGGCTTGGATCCTGGGCTGGGTGGCCCCTGTCTCGGGGCTTGCCCCACTCTGCCTGCCTGCTGTTGGTCCTCTCTCTGTGGGGCTGA Homo sapiens hg19 +GNAS1.chr20.57484420.57484421_tile_1 GNAS1.chr20.57484420.57484421_tile_1 1 chr20 57484390 57484560 + TGCCGTGTCCTGACTTCTGGAATCTTTGAGACCAAGTTCCAGGTGGACAAAGTCAACTTCCAGTAAGCCAACTGTTACCTTTTTATATAACAGAGATCATGGTTTCTTGACATTCAC Homo sapiens hg19 +SMARCB1_1.chr22.24133967.24133990_tile_1 SMARCB1_1.chr22.24133967.24133990_tile_1 1 chr22 24133939 24134126 + TCCGAGGTTCTCTGTACAAGAGATACCCCTCACTCTGGAGGCGACTAGCCACTGTGGAAGAGAGGAAGAAAATAGTTGCATCGTCACATGGTAAAAAAACAAAACCTAACACTAAGGGTGCGTCTTCACGAGGGTT Homo sapiens hg19 +SMARCB1_3.chr22.24143240.24143240_tile_1 SMARCB1_3.chr22.24143240.24143240_tile_1 1 chr22 24143210 24143383 + GGGCCGAGACAAGAAGAGAACCTTCCCCCTTTGGTGTGGATGCATCGCTGCACTCACCCTCCGTGCTGATTCCGCCTTAGTTCTCCAGCACGTTTCAGTTCCTTCCTCCCCAGAAAAACACT Homo sapiens hg19 +SMARCB1_4.chr22.24145582.24145582_tile_1 SMARCB1_4.chr22.24145582.24145582_tile_1 1 chr22 24145552 24145726 + GCTGCGAGACGCCTTCACCTGGAACATGAATGGTACAAGGCAGTCGGGCTTGGCTGGGCCTGGCCCCAACCCCTGTGTGTTACGTGGGAACAGTCCCGTTTCCTGCCAGCTGCCTGTCAGGC Homo sapiens hg19 +SMARCB1_5_6.chr22.24176352.24176357_tile_1 SMARCB1_5_6.chr22.24176352.24176357_tile_1 1 chr22 24176324 24176495 + CGGCCCCGGCCTGGTAACCAGCCCATCAGCACACGGCTCCCACGGAGCATCTCAGAAGATTGGGCCGCCTCTCCTCCATCTTCTGGCAAGGACAGAGGCGAGGGGACAGCCCAGCGCCA Homo sapiens hg19 +GNA11_4.chr19.3114942.3115070_tile_1 GNA11_4.chr19.3114942.3115070_tile_1 1 chr19 3114824 3115004 - GTAGCCCAAGGTGGCGATGCGGTCAACGTCGGTCAGGTAGCTGCAACACAGCGGTGGGTGCTCAGGCCGGCTGCCGGGGGTGGGGGGGCAGGACAGGGACACAGCACCCAAACCAGCGGGAGGACGGAAAGCCACC Homo sapiens hg19 +GNA11_4.chr19.3114942.3115070_tile_2 GNA11_4.chr19.3114942.3115070_tile_2 1 chr19 3114958 3115133 + CCTGCCCACCCAGCAGGACGTGCTGCGGGTCCGCGTGCCCACCACCGGCATCATCGAGTACCCTTTCGACCTGGAGAACATCATCTTCCGGTACCGCCCGGGCCACAGCAGGCGGGGAGGGGGCACTGAGA Homo sapiens hg19 +GNA11_5.chr19.3118922.3119051_tile_1 GNA11_5.chr19.3118922.3119051_tile_1 1 chr19 3118802 3118989 - CACTTCCTCCGCTCCGACCGCTGGCCCCCCACATCCACCATCCTGAAAGGACACAGCGCCAGGACTCAGCCACCTGGCGCCCCAAGGCCCAATCTGCAATCCCAGGACGGCTCCCACCCAAGCCCCTCCTGCCACACC Homo sapiens hg19 +GNA11_6.chr19.3119204.3119357_tile_2 GNA11_6.chr19.3119204.3119357_tile_2 1 chr19 3119208 3119395 - CCGCAGCCCGGCGCACCATCGAACTCGGGGAAGTAGTCCACCAGGTGCGAGTACAGGATCTTGTCCTCCAGCAGGTCCTTCTTGTTGAGGAAGAGGATGACGGAGGAGTTCTGGAACCAGGGGTAGGTGATGATGGTCCGG Homo sapiens hg19 +GNA11_7.chr19.3120987.3121177_tile_1 GNA11_7.chr19.3120987.3121177_tile_1 1 chr19 3120865 3121035 + GGGCCTTACTCGCTCATCCCCTGGGAGTGACAAAGGGGCCCACGAGTCCCTTGCCCTGGGCCGGGCTGGGGCACAGCCTCACCCTCTGCCCTCCCCCAGGTCCCCAGCGGGACGCCCAGGC Homo sapiens hg19 +GNA11_7.chr19.3120987.3121177_tile_2 GNA11_7.chr19.3120987.3121177_tile_2 1 chr19 3120985 3121170 - CAGGATGGTGTCCTTCACGGCCGCGAACACGAAGCGGATGTTCTCCGTGTCGGTGGCACACGTGAAGTGTGAGTAGATGATCTTGTCGCTGTCGGGGTTCAGGTCCACGAACATCTTCAGGATGAACTCCCGCGCCGC Homo sapiens hg19 +GNA11_7.chr19.3120987.3121177_tile_3 GNA11_7.chr19.3120987.3121177_tile_3 1 chr19 3121121 3121304 + GCAGCTCAACCTCAAGGAGTACAACCTGGTCTGAGCGCCCAGGCCCAGGGAGACGGGATGGAGACACGGGGCAGGACCTTCCTTCCACGGAGCCTGCGGCTGCCGGGCGGGTGGCGCTGCCGAGTCCGGGCCGGGGC Homo sapiens hg19 +GNAQ_4.chr9.80412436.80412564_tile_1 GNAQ_4.chr9.80412436.80412564_tile_1 1 chr9 80412406 80412592 + TACCTGAAAATGACACTTTGTAAGTCAAAGGGGTATTCGATGATCCCTGTGGTGGGGACTCGAACTCTAAGCACATCTTGTTGCGTAGGCAGGTAGGCAGGGTCAGCTACGCGGTCCAAGTCATTAAGATAGC Homo sapiens hg19 +GNAQ_5.chr9.80409379.80409508_tile_1 GNAQ_5.chr9.80409379.80409508_tile_1 1 chr9 80409249 80409421 + AAAGAAGTAAGTTCACTCCATTCCCCACACCCTACTTTCTATCATTTACTTGTATCAGATAATAAAATGATAATCCATTGCCTGTCTAAAGAACACTTACCTCATTGTCTGACT Homo sapiens hg19 +GNAQ_5.chr9.80409379.80409508_tile_2 GNAQ_5.chr9.80409379.80409508_tile_2 1 chr9 80409335 80409510 - AGGTCAGAGAGAAGAAAATGGATACACTGCTTTGAAAATGTCACCTCTATCATGTTTCTAGTAGCGCTTAGTGAATATGATCAAGTTCTCGTGGAGTCAGACAATGAGGTAAGTGTTCTTTA Homo sapiens hg19 +GNAQ_5.chr9.80409379.80409508_tile_3 GNAQ_5.chr9.80409379.80409508_tile_3 1 chr9 80409459 80409639 + TTTGGCCCCCTACATCGACCATTCTGCAAGGTTAACAATACTCATATTAATAACATATAAAGTAAAACTAAAAAGTCAACATAAATATAGCACTACTTACAAACTTAGGGAAAATATTCTCTTGAAT Homo sapiens hg19 +GNAQ_6.chr9.80343430.80343583_tile_1 GNAQ_6.chr9.80343430.80343583_tile_1 1 chr9 80343306 80343476 + GGGCAGCAATGGTGCACTGTAGTGCGTTAACTCCCACACTGGGGTTTGGAGACAAAACCTATTCACAGCTACTGAGCTGTGGTATGAGTGCTGACTTACCATCATATTCTGGGAAGT Homo sapiens hg19 +GNAQ_6.chr9.80343430.80343583_tile_2 GNAQ_6.chr9.80343430.80343583_tile_2 1 chr9 80343392 80343561 - GGTTCCAGAACTCCTCGGTTATTCTGTTCTTAAACAAGAAAGATCTTCTAGAGGAGAAAATCATGTATTCCCATCTAGTCGACTACTTCCCAGAATATGATGGTAAGTCAGCAC Homo sapiens hg19 +GNAQ_6.chr9.80343430.80343583_tile_3 GNAQ_6.chr9.80343430.80343583_tile_3 1 chr9 80343504 80343689 + CAGGGGTATGTGATAATTGTTCTAAAGAGAGCCTTGCTTTCCTCCATTCGGTTCTGGAAAAAAAAAAAAAATCAGAAAAAACAAGGAGTGAATTACATGATTACTTAATTTGTGAATTGTGTTTATTTT Homo sapiens hg19 +GNAQ_7.chr9.80336240.80336429_tile_1 GNAQ_7.chr9.80336240.80336429_tile_1 1 chr9 80336110 80336280 + TTAGTATTATGCAAATTGTTTTCCACAGAAATACAGTCCCTCTTGTGTATCTTCAATAGCCCACCAGGGAAGGGCAGGGCGGGTGTCTAGGAGGCACAATTAGACCAGATTGTACT Homo sapiens hg19 +GNAQ_7.chr9.80336240.80336429_tile_2 GNAQ_7.chr9.80336240.80336429_tile_2 1 chr9 80336204 80336374 - CTACTCCCACTTCACGTGCGCCACAGACACCGAGAATATCCGCTTTGTCTTTGCTGCCGTCAAGGACACCATCCTCCAGTTGAACCTGAAGGAGTACAATCTGGTCTAATTGTGCCTCC Homo sapiens hg19 +GNAQ_7.chr9.80336240.80336429_tile_3 GNAQ_7.chr9.80336240.80336429_tile_3 1 chr9 80336320 80336495 + GATAATTTTGTCACTGTCTGGGTTCAGGTCCACGAACATCTTCAGAATGAATTCTCGGGCTGCCTGGGCATCTCTCTGGGGTCCTTTCGGCCAAGAGACAAGAGGGACACTTTGTTACCTA Homo sapiens hg19 +PIK3CA4_11.chr3.178936074.178936095_tile_1 PIK3CA4_11.chr3.178936074.178936095_tile_1 2 chr22 17052964 17053133 + ATCCTCTCTCTGAAATCACTGCGCAGGAGAAAGATTTTCTATGGACCACAGGTAAGTGCTAAAATGGAGATTCTCTGTTTCTTTTTCTTTATTACAGAAAAAATAACTGACTTTGG Homo sapiens hg19 +PIK3CA12.chr3.178938860.178938860_tile_1 PIK3CA12.chr3.178938860.178938860_tile_1 2 chr22 17055413 17055585 + CACCTGAATAGGCAAGTCGAGGCAATGGAAAAGCTCATTAACTTAACTGACATTGTCAAACAGGAGAAGAAGGATGAAACACAAAAGTTGTGTGACTCTAGTCTGTGTTTGAGACTCTT Homo sapiens hg19 +PTEN7.chr10.89717615.89717772_tile_1 PTEN3.chr10.89685307.89685307_tile_1 2 chr9 33675957 33676480 - ATACACAATCTTTGTGCTGAAAGACATTATGACACCGCCAAATCTAATTACAGAGTTGCGCAATATCCTTTTGAAGACCATAACCCACCACAGCTAGAACTTATCAAACCCTTTTGTGAAGATCTTGACCAATGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCACTGTAAAGCTGGAAAGGGACGAACTGGTATAATGATTTATGCATATTTATTACATCGGGGCAAATTTTTAAAGGCACAAGAGGCCCTAGATTTCTATGGGGAAGTAAGGACCAGAGACAAAAAGGGAGTAACTATTCCCAGTCAGAGGCGCTATGTGTATTACTATAGCTACCTGGTAAAGAATCATGTGGATTATAGACCAGTGGCACTGTTGTTTCACAAGATGATGTTTGAAACTATTCCAATGTTCAGTGGCGGAACTTGCAATCCTCAGTTTGTGGTCTGCCAGCTAAAG Homo sapiens hg19 +PTEN13.chr10.89720716.89720852_tile_1 PTEN13.chr10.89720716.89720852_tile_1 2 chr9 33675629 33675815 - CAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATTGATAGCATTTGCAGTATAGAGCGTGCAGATAATGACAAGGAGTATCTAGTACTTACTTTAACAAAAAATGATCTTGACAAAGCAAATAAAGACA Homo sapiens hg19 +GNA11_6.chr19.3119204.3119357_tile_2 GNA11_7.chr19.3120987.3121177_tile_2 2 chr7 65970150 65970483 + CAGGATGGTGTCCTTCACGGCCGCGAACACGAAGCGGATGTTCTTCGTGTCGGTGGCGTACGTGAAGTGGGAGTCGATGATCTTGTCGCTGTCGGGGTTCATGTCCACTAACATCTTCAGGATGAACTCCCGCGCCGCCTGGGCGTCCTGCTGGGGCCCTTCGAACTCGGGGAAGTAGTCCACCATGTGTGAGTACAGGATATTGTCCTCCAGCAGGTCCTTCTTGTTGAGGAAGGTGATGACGGGGGAGTTCTGGAACCAGGGGTAGTCGATGATGGTCCGG Homo sapiens hg19 +GNA11_7.chr19.3120987.3121177_tile_1 GNA11_4.chr19.3114942.3115070_tile_2 2 chr7 65970285 65970719 - CCTGCCCACCCAGCAGGACGTGCTGCGGGTCCGCGTGCCCACCACCGGCGTCTTTCGACCTGGAGAACATCATCTTCAGGATGGCGGATGTTGGGGGACAGCGGTCGGCGCAGAGGAAGTGGATCCACTGCTTTGAGAACCTGACGTCCATCCCGTTTCTCGTCGCCCTCAGTGAATACGACCAAGTCCTGGTGGAGTCGGACAACGAGAACCGGATGGAGGAGAGCAAAGCCCTGTTCCGGACCATCATCGACTACCCCTGGTTCCAGAACTCCCCCGTCATCACCTTCCTCAACAAGAAGGACCTGCTGGAGGACAATATCCTGTACTCACACATGGTGGACTACTTCCCCGAGTTCGAAGGGCCCCAGCAGGACGCCCAGGC Homo sapiens hg19 +GNAQ_5.chr9.80409379.80409508_tile_1 GNAQ_7.chr9.80336240.80336429_tile_1 2 chr2 132181238 132181750 + TTAGTATTATGCAAATTGTTTTCCACAGAAATACAGTCCCTCTTGTGTATCTTCAATAGCCCACCATGGAAGGGCAGGGCGGGTGTCTAGGAGGCACAACTAGACCAGATTGTAATCCTTCAGGTTCAACTGGAGGATGGTGTCCTTGACGGCAGCAAACACAAAGCGGATATTCTCGGTGTCTGTGGCGCATGTGAAGTGGGAGTAGATAATTTGGTCACTGGGTTCAGGTCCACGAACATCTTCAGAATGAATTCTCGGGCTGCCTGGGCATCTCTCTGGGGTCCATCATATTCTGGGAAGTAGTCGACTAGATGGGAATACATGATTTTCTCCTCTGGAAGATCTTTCTTGTTTAACAACAGAATAACCGAGGAGTTCTGGAACCAGGGATACGTGATAATTGTACTAAAGAGAGCCTTGCTTTCCTCCATTCGGTTCTCATTGTCTGACT Homo sapiens hg19 +GNAQ_6.chr9.80343430.80343583_tile_1 GNAQ_7.chr9.80336240.80336429_tile_3 2 chr2 132181448 132181600 + GATAATTTGGTCACTGGGTTCAGGTCCACGAACATCTTCAGAATGAATTCTCGGGCTGCCTGGGCATCTCTCTGGGGTCCATCATATTCTGGGAAGT Homo sapiens hg19 +GNAQ_7.chr9.80336240.80336429_tile_2 GNAQ_5.chr9.80409379.80409508_tile_2 2 chr2 132181332 132181839 - AGGTCAGAGAGAAGAAAATGGATACACTGCTTTGAAAATGTCACCTCTATCATGTTTCTAGTAGCGCTTAGTGAATATGATCGAGTTCTCGTGGAGTCAGACAATGAGAACCGAATGGAGGAAAGCAAGGCTCTCTTTAGTACAATTATCACGTATCCCTGGTTCCAGAACTCCTCGGTTATTCTGTTGTTAAACAAGAAAGATCTTCCAGAGGAGAAAATCATGTATTCCCATCTAGTCGACTACTTCCCAGAATATGATGGACCCCAGAGAGATGCCCAGGCAGCCCGAGAATTCATTCTGAAGATGTTCGTGGACCTGAACCCAGTGACCAAATTATCTACTCCCACTTCACATGCGCCACAGACACCGAGAATATCCGCTTTGTGTTTGCTGCCGTCAAGGACACCATCCTCCAGTTGAACCTGAAGGATTACAATCTGGTCTAGTTGTGCCTCC Homo sapiens hg19 diff -r 1b81dd6b68b5 -r 9285f791716d tool_dependencies_MAINTOOLSHED.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies_MAINTOOLSHED.xml Thu Sep 11 05:11:11 2014 -0400 @@ -0,0 +1,30 @@ + + + + + + Let's see where this msg appears...R + + + + + Let's see where this msg appears...samtools + + + + + Let's see where this msg appears...snpeff + + + + + Let's see where this msg appears...varscan + + + + + $REPOSITORY_INSTALL_DIR + Let's see where this msg appears...ENV VAR + + +