Mercurial > repos > stef > falco
changeset 34:b51c36920d7b draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 10 Oct 2014 10:13:55 -0400 |
| parents | 12f7ce7de71f |
| children | 8bc2e1a67449 |
| files | falco/misc/init.sh |
| diffstat | 1 files changed, 57 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/misc/init.sh Fri Oct 10 10:13:55 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