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author stef
date Fri, 10 Oct 2014 09:50:26 -0400
parents 3419fc808193
children f1b32c09deaf
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#!/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