config.hg19.ini

[TOOLS]
PYTHON3  = {ENVDIR}/bin/python3
SYNAPSE  = {ENVDIR}/bin/synapse
AWS      = {ENVDIR}/bin/aws
JAVA     = {ENVDIR}/bin/java
BWA      = {ENVDIR}/bin/bwa
SAMTOOLS = {ENVDIR}/bin/samtools
SAMBAMBA = {ENVDIR}/bin/sambamba
GATK     = {ENVDIR}/bin/GenomeAnalysisTK
GATK4    = {ENVDIR}/bin/gatk
PICARD   = {ENVDIR}/bin/picard
BGZIP    = {ENVDIR}/bin/bgzip
TABIX    = {ENVDIR}/bin/tabix
VT       = {ENVDIR}/bin/vt
BCFTOOLS = {ENVDIR}/bin/bcftools
ROOTSYS  = {ENVDIR}
CNVNATOR = {ENVDIR}/bin/cnvnator
LIFTOVER = {ENVDIR}/bin/liftOver
MFDIR    = {ENVDIR}/MosaicForecast

[RESOURCES]
REFDIR         = {PIPEHOME}/resources/hg19
REF            = {PIPEHOME}/resources/hg19/ucsc.hg19.fasta
DBSNP          = {PIPEHOME}/resources/hg19/dbsnp_138.hg19.vcf.gz
MILLS          = {PIPEHOME}/resources/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz
INDEL1KG       = {PIPEHOME}/resources/hg19/1000G_phase1.indels.hg19.sites.vcf.gz
OMNI           = {PIPEHOME}/resources/hg19/1000G_omni2.5.hg19.sites.vcf.gz
HAPMAP         = {PIPEHOME}/resources/hg19/hapmap_3.3.hg19.sites.vcf.gz
SNP1KG         = {PIPEHOME}/resources/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf.gz
MASK1KG        = {PIPEHOME}/resources/hg19/1KG.20141020.strict_mask.hg19_GRCh37.fa.gz
GNOMAD_SNP     = {PIPEHOME}/resources/hg19/gnomAD.r2.1.1.AFover0.001.snps.txt.gz
PONFA          = {PIPEHOME}/resources/PON.q20q20.05.5.fa
HG19_TO_HG38   = {PIPEHOME}/resources/hg19ToHg38.over.chain.gz
MFRES          = {PIPEHOME}/resources/hg19