【群体遗传】LDdecay计算和做图

2024年5月4日发(作者：)

sample:

# 1) For gatk VCF file deal , run PopLDdecay direct

./bin/PopLDdecay -InVCF -OutStat

# 2) For plink [.ped .map], chang plink 2 genotype first 2) run PopLDdecay

perl bin/mis/ -inPED -inMAP -outGenotype pe ; ./bin/PopLDdecay -InGenotype pe -OutStat

# 3) To Calculate the subgroup GroupA LDdecay in VCF Files # put GroupA sample names into GroupA_ file

./bin/PopLDdecay -InVCF -OutStat -SubPop GroupA_

step2:

sample: