ON/OFF=ON
seqbility_bin=/PAPipe/Programs/msmc/mappability/seqbility-20091110
msmctools_bin=/PAPipe/Programs/msmc/msmc-tools
msmc_path=msmc2_Linux
samtools_path=samtools
bwa_path=bwa
python_path=python3
faSize=faSize
bcftools_path=bcftools
ref_fa=/RUN_DOCKER/data/ref/cow.chr1.fa
threads=20
i=20
r=0.25
p=1*2+25*1+1*2+1*3
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