gatk_references.sh

export DBSNP=~/nesi00319/reference_files/dbsnp_138.b37.vcf
export MILLS=~/nesi00319/reference_files/Mills_and_1000G_gold_standard.indels.b37.vcf
export INDELS=~/nesi00319/reference_files/1000G_phase1.indels.b37.vcf
export REF=~/nesi00319/reference_files/hs37d5/hs37d5.fa


#########################
# GrCh37 Gender regions #
#########################

export XPAR1="X:1-2699520"
export TRUEX="X:2699521-154931043"
export XPAR2="X:154931044-155260560"
export TRUEY="Y:2649521-59034050"