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path_file.sh
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path_file.sh
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#################
# REFERENCE FILES
#################
REF=/home/sam/HOPP-Informatics/projects/sequencingPipeline/refs/Homo_sapiens_assembly19.fasta
#REF=/home/sam/HOPP-Informatics/projects/sequencingPipeline/refs/GRCh37-lite.fa
COSMICVCF=/home/sam/HOPP-Informatics/projects/sequencingPipeline/refs/hg19_cosmic_v54_120711.vcf
DBSNPVCF=/home/sam/HOPP-Informatics/projects/sequencingPipeline/refs/dbsnp_132_b37.leftAligned.vcf
VCF_ALL=/home/sam/HOPP-Informatics/projects/sequencingPipeline/refs/00-All.vcf
######
# JAVA
######
JAVA=/usr/bin/java
#########
# ANNOVAR
#########
ANNOVAR_PATH=/hopp-storage/HOPP-TOOLS/ANNOTATIONS/annovar/annotate_variation.pl
ANNOVAR_DB=/hopp-storage/HOPP-TOOLS/ANNOTATIONS/annovar/humandb/
ANNOVAR0=/hopp-storage/HOPP-TOOLS/ANNOTATIONS/annovar/convert2annovar.pl
ANNOVAR="/hopp-storage/HOPP-TOOLS/ANNOTATIONS/annovar-may-2013/annovar/annotate_variation.pl -buildver hg19"
ANNOVAR_DB=/hopp-storage/HOPP-TOOLS/ANNOTATIONS/annovar-may-2013/annovar/humandb
######
# GATK
######
GATK=/home/sam/tools/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar
SomaticIndelDetector=/home/sam/tools/Somatic-Indel-Detector/dist/GenomeAnalysisTK.jar
#GAT1=/home/sam/tools/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar
#GAT0=/home/sam/tools/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar
#GATK=/hopp-storage/HOPP-TOOLS/PIPELINES/GATKBundle/GenomeAnalysisTK-2.4-9-g532efad/GenomeAnalysisTK.jar
#GAT1=/hopp-storage/HOPP-TOOLS/PIPELINES/GATKBundle/Somatic-Indel-Detector/GATK/dist/GenomeAnalysisTK.jar
#GAT0=/hopp-storage/HOPP-TOOLS/PIPELINES/GATKBundle/Sting/dist/GenomeAnalysisTK.jar # Use old GATK for identifying target intervals
########
# MUTECT
########
MUTECT=/home/sam/tools/muTect-source-4.21.2015/mutect/target/mutect-1.1.7.jar
##########
# SAMTOOLS
##########
SAM=/home/sam/tools/samtools-1.1/samtools
########
# PICARD
########
PIC=/hopp-storage/HOPP-TOOLS/PIPELINES/GATKBundle/picard-tools-1.46/
########
# SNPEFF
########
SNPEFF=/hopp-storage/HOPP-TOOLS/ANNOTATIONS/snpEff/SnpSift.jar
##############################
# annotation execution scripts
##############################
# 1000g_ANNO=/hopp-storage/HOPP-TOOLS/PIPELINES/MutPipelines/scripts/annotate-100g-calls.sh <------ missing
# ESP_ANNO=/hopp-storage/HOPP-TOOLS/PIPELINES/MutPipelines/scripts/annotate-ESP-calls.sh <------ missing
# dbSNP_ANNO=/hopp-storage/HOPP-TOOLS/PIPELINES/MutPipelines/scripts/annotate-dbSNP-calls.sh <------ missing
# COSMIC_ANNO=/HOPP-Informatics/projects/sequencingPipeline/scripts/annotate-cosmic-calls.sh