changeset 35:8bc2e1a67449 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/falco/misc/amplicon-VcAn-TSACP.sh	Fri Oct 10 10:45:56 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