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variants_pipeline_config.txt
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variants_pipeline_config.txt
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SINGULARITY /opt/local/singularity/2.6.0/bin/
ABRA /opt/common/CentOS_6/abra2/abra2-2.17
BCFTOOLS /opt/common/CentOS_6/bcftools/bcftools-1.2/bin
BEDTOOLS /opt/common/CentOS_6/bedtools/bedtools-2.22.0/bin
BWA /opt/common/CentOS_6/bwa/bwa-0.7.12
CUTADAPT /opt/common/CentOS_6/cutadapt/cutadapt-1.9.1/bin
DELLY /opt/common/CentOS_6/delly/delly-master-9b7fc59
dRANGER /opt/common/CentOS_6/dranger/dRanger_annotate_v2.0
HTSTOOLS /opt/common/CentOS_6/htstools/htstools_0.1.1
FACETS_SUITE /juno/opt/common/CentOS_6/facets-suite/facets-suite-2.0.6
FIXMULTIINDEL /opt/common/CentOS_6/FixMultiInDel/FixMultiInDel-2.0.1
GATK /opt/common/CentOS_6/gatk/GenomeAnalysisTK-3.4-0-g7e26428
GATK4 /opt/common/CentOS_6/gatk/gatk-4.1.1.0
JAVA /opt/common/CentOS_6/java/jdk1.8.0_31/bin
JAVA7_MUTECT /opt/common/CentOS_6/java/jdk1.7.0_75/bin
LANCET /opt/common/CentOS_6/lancet/lancet-1.0.4
MANTA /opt/common/bic/manta/bin
MCR /opt/common/CentOS_6/matlab/v81
MUTECT /opt/common/CentOS_6/muTect/muTect-1.1.7
PERL /opt/common/CentOS_6/perl/perl-5.22.0/bin
PICARD /opt/common/CentOS_6/picard/picard-tools-1.124
PINDEL /opt/common/CentOS_6/pindel/pindel-0.2.5b9
PYTHON /opt/common/CentOS_6/python/python-2.7.8/bin
R /opt/common/CentOS_6/R/R-3.1.2/bin
R_FACETS /juno/opt/common/CentOS_7-dev/R/R-3.5.1/bin
SAMTOOLS /opt/common/CentOS_6/samtools/samtools-1.2
SCALPEL /opt/common/CentOS_6/scalpel/scalpel-0.2.2
SOMATICSNIPER /opt/common/CentOS_6/somaticsniper/somatic-sniper-1.0.4
STRELKA /opt/common/CentOS_6/strelka/strelka_1.0.11
TABIX /opt/common/CentOS_6/samtools/samtools-1.2/htslib-1.2.1
VARDICT_JAVA /opt/common/CentOS_6/VarDictJava/VarDict-1.5.1/bin
VARDICT_PERL /opt/common/CentOS_6/VarDict/VarDict_85cc3f6
VARSCAN /opt/common/CentOS_6/varscan/v2.3.7
VCF2MAF /opt/common/CentOS_7/vcf2maf/vcf2maf-1.6.21
VCFTOOLS /opt/common/CentOS_6-dev/vcftools/v0.1.14/bin
VEP /opt/common/CentOS_7/vep/ensembl-vep-release-102
VIRMID /opt/common/CentOS_6/virmid/Virmid-1.1.1
WES_FILTER /opt/common/CentOS_6/wes-filter/wes-filters-1.1.3
B37_BWA_INDEX /juno/depot/assemblies/H.sapiens/b37/index/bwa/0.7.12/b37.fasta
B37_FASTA /juno/depot/assemblies/H.sapiens/b37/b37.fasta
B37_FAI /juno/depot/assemblies/H.sapiens/b37/b37.fasta.fai
B37_MM10_HYBRID_BWA_INDEX /juno/depot/assemblies/hybrids/H.sapiens_M.musculus/b37_mm10/index/bwa/0.7.12/b37_mm10.fasta
B37_MM10_HYBRID_FASTA /juno/depot/assemblies/hybrids/H.sapiens_M.musculus/b37_mm10/b37_mm10.fasta
B37_MM10_HYBRID_FAI /juno/depot/assemblies/hybrids/H.sapiens_M.musculus/b37_mm10/b37_mm10.fasta.fai
HG19_BWA_INDEX /juno/depot/assemblies/H.sapiens/hg19/index/bwa/0.7.4-r385/hg19.fasta
HG19_FASTA /juno/depot/assemblies/H.sapiens/hg19/hg19.fasta
HG19_FAI /juno/depot/assemblies/H.sapiens/hg19/hg19.fasta.fai
HG19_MM10_HYBRID_BWA_INDEX /juno/depot/assemblies/hybrids/H.sapiens_M.musculus/hg19_mm10/index/bwa/0.7.8/hg19_mm10.fasta
HG19_MM10_HYBRID_FASTA /juno/depot/assemblies/hybrids/H.sapiens_M.musculus/hg19_mm10/hg19_mm10.fasta
HG19_MM10_HYBRID_FAI /juno/depot/assemblies/hybrids/H.sapiens_M.musculus/hg19_mm10/hg19_mm10.fasta.fai
MM9_BWA_INDEX /juno/depot/assemblies/M.musculus/mm9/index/bwa/0.7.4-r385/mm9.fasta
MM9_FASTA /juno/depot/assemblies/M.musculus/mm9/mm9.fasta
MM9_FAI /juno/depot/assemblies/M.musculus/mm9/mm9.fasta.fai
MM10_BWA_INDEX /juno/depot/assemblies/M.musculus/mm10/index/bwa/0.7.8/mm10.fasta
MM10_FASTA /juno/depot/assemblies/M.musculus/mm10/mm10.fasta
MM10_FAI /juno/depot/assemblies/M.musculus/mm10/mm10.fasta.fai
MM10_B37_HYBRID_BWA_INDEX /juno/depot/assemblies/hybrids/M.musculus_H.sapiens/mm10_b37/index/bwa/0.7.12/mm10_b37.fasta
MM10_B37_HYBRID_FASTA /juno/depot/assemblies/hybrids/M.musculus_H.sapiens/mm10_b37/mm10_b37.fasta
MM10_B37_HYBRID_FAI /juno/depot/assemblies/hybrids/M.musculus_H.sapiens/mm10_b37/mm10_b37.fasta.fai
MM10_HG19_HYBRID_BWA_INDEX /juno/depot/assemblies/hybrids/M.musculus_H.sapiens/mm10_hg19/index/bwa/0.7.12/mm10_hg19.fasta
MM10_HG19_HYBRID_FASTA /juno/depot/assemblies/hybrids/M.musculus_H.sapiens/mm10_hg19/mm10_hg19.fasta
MM10_HG19_HYBRID_FAI /juno/depot/assemblies/hybrids/M.musculus_H.sapiens/mm10_hg19/mm10_hg19.fasta.fai
MM10_CUSTOM_BWA_INDEX
MM10_CUSTOM_FASTA
MM10_CUSTOM_FAI
SPECIES_CUSTOM_BWA_INDEX
SPECIES_CUSTOM_FASTA
SPECIES_CUSTOM_FAI
SPECIES_CUSTOM_DB_SNP
DM6_BWA_INDEX /juno/depot/assemblies/D.melanogaster/dm6/index/bwa/0.7.12/dm6.fasta
DM6_FASTA /juno/depot/assemblies/D.melanogaster/dm6/dm6.fasta