vcf=Sample.pass.vcf
samplelist=sample.txt

##1. Sample sort and filter
vcf_sort_filter.py ${vcf} ${vcf%%.*}_sort.vcf -f ${samplelist} -a 

##2.
vcf2genotype.py -i ${vcf%%.*}_sort.vcf -o ${vcf%%.*}_sort.geno

##3.
hgmap_treat.py ${vcf%%.*}_sort.geno -o ${vcf%%.*}_sort

##4.
hgmap_merge.py ${vcf%%.*}_sort.raw -o ${vcf%%.*}_sort

##5.
hgmap_chiqtest.py ${vcf%%.*}_sort_subBin.wraw -o ${vcf%%.*}_sort_subBin 
