ON/OFF=ON
VCFUTILS=vcfutils.pl
SAMTOOLS=samtools
BCFTOOLS=bcftools
PSMC_DIR=/PAPipe/Programs/psmc/
Reference=/RUN_DOCKER/data/ref/cow.chr1.fa
q=20
SAM_C=50
VCF_d=10
VCF_D=100
N=25
t=15
r=5
p=4+25*2+4+6
BAM_Hanwoo_Hanwoo1=./out/01_ReadMapping/04.ReadRegrouping/Hanwoo_Hanwoo1.addRG.marked.sort.bam
BAM_Holstein_Holstein5=./out/01_ReadMapping/04.ReadRegrouping/Holstein_Holstein5.addRG.marked.sort.bam
BAM_Holstein_Holstein1=./out/01_ReadMapping/04.ReadRegrouping/Holstein_Holstein1.addRG.marked.sort.bam
BAM_Angus_Angus4=./out/01_ReadMapping/04.ReadRegrouping/Angus_Angus4.addRG.marked.sort.bam
BAM_Jersey_Jersey4=./out/01_ReadMapping/04.ReadRegrouping/Jersey_Jersey4.addRG.marked.sort.bam
BAM_Holstein_Holstein4=./out/01_ReadMapping/04.ReadRegrouping/Holstein_Holstein4.addRG.marked.sort.bam
BAM_Hanwoo_Hanwoo2=./out/01_ReadMapping/04.ReadRegrouping/Hanwoo_Hanwoo2.addRG.marked.sort.bam
BAM_Holstein_Holstein3=./out/01_ReadMapping/04.ReadRegrouping/Holstein_Holstein3.addRG.marked.sort.bam
BAM_Jersey_Jersey2=./out/01_ReadMapping/04.ReadRegrouping/Jersey_Jersey2.addRG.marked.sort.bam
BAM_Jersey_Jersey3=./out/01_ReadMapping/04.ReadRegrouping/Jersey_Jersey3.addRG.marked.sort.bam
BAM_Hanwoo_Hanwoo5=./out/01_ReadMapping/04.ReadRegrouping/Hanwoo_Hanwoo5.addRG.marked.sort.bam
BAM_Holstein_Holstein2=./out/01_ReadMapping/04.ReadRegrouping/Holstein_Holstein2.addRG.marked.sort.bam
BAM_Jersey_Jersey1=./out/01_ReadMapping/04.ReadRegrouping/Jersey_Jersey1.addRG.marked.sort.bam
BAM_Hanwoo_Hanwoo3=./out/01_ReadMapping/04.ReadRegrouping/Hanwoo_Hanwoo3.addRG.marked.sort.bam
BAM_Jersey_Jersey5=./out/01_ReadMapping/04.ReadRegrouping/Jersey_Jersey5.addRG.marked.sort.bam
BAM_Angus_Angus2=./out/01_ReadMapping/04.ReadRegrouping/Angus_Angus2.addRG.marked.sort.bam
BAM_Angus_Angus1=./out/01_ReadMapping/04.ReadRegrouping/Angus_Angus1.addRG.marked.sort.bam
BAM_Angus_Angus5=./out/01_ReadMapping/04.ReadRegrouping/Angus_Angus5.addRG.marked.sort.bam
BAM_Angus_Angus3=./out/01_ReadMapping/04.ReadRegrouping/Angus_Angus3.addRG.marked.sort.bam
BAM_Hanwoo_Hanwoo4=./out/01_ReadMapping/04.ReadRegrouping/Hanwoo_Hanwoo4.addRG.marked.sort.bam
BAM_Simmental_Simmental1=./out/01_ReadMapping/04.ReadRegrouping/Simmental_Simmental1.addRG.marked.sort.bam
BAM_Simmental_Simmental2=./out/01_ReadMapping/04.ReadRegrouping/Simmental_Simmental2.addRG.marked.sort.bam
BAM_Simmental_Simmental3=./out/01_ReadMapping/04.ReadRegrouping/Simmental_Simmental3.addRG.marked.sort.bam
BAM_Simmental_Simmental4=./out/01_ReadMapping/04.ReadRegrouping/Simmental_Simmental4.addRG.marked.sort.bam
BAM_Simmental_Simmental5=./out/01_ReadMapping/04.ReadRegrouping/Simmental_Simmental5.addRG.marked.sort.bam