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changeset 28:d3a63172c5a7 draft

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Uploaded
author stef
date Fri, 10 Oct 2014 06:26:38 -0400
parents bff3cf6954f7
children 02e5aee670de
files falco/init.sh
diffstat 1 files changed, 18 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/falco/init.sh	Fri Oct 10 06:26:11 2014 -0400
+++ b/falco/init.sh	Fri Oct 10 06:26:38 2014 -0400
@@ -2,27 +2,27 @@
 
 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
+#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
+#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
+#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
@@ -31,8 +31,8 @@
 
 #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
+#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