群体遗传学三-LD

使用PopLDdecay进行LD值的计算及绘图

#popLDdecay
cd /public/home/*/data/test
#step1:
#1.For gatk VCF file deal , run PopLDdecay  direct
PopLDdecay -InVCF SNP.vcf.gz -OutStat Lddecay.stat.gz  
#2.For plink [.ped .map], chang plink 2 genotype first  2) run PopLDdecay 
#perl plink2genotype.pl -inPED in.ped -inMAP in.map -outGenotype out.genotype      
#PopLDdecay -InGenotype out.genotype -OutStat LDdecay.stat.gz
#3.To Calculate the subgroup GroupA LDdecay in VCF Files   # put GroupA sample names into GroupA_sample.list file
#PopLDdecay -InVCF -OutStat -SubPop GroupA_sample.list
#step2
#1.For one Population
perl Plot_OnePop.pl -inFile Lddecay.stat.gz -output Fig
#2.For one Population muti chr
#pelr bin/Plot_OnePop.pl -inList Chr.reslutPath.list -output Fig
#3.For muti Population
#pelr bin/Plot_OnePop.pl -inList Pop.reslutPath.list -output Fig