Hi I'm studying about sequencing data analysis. I performed a series of analysis and i finally get multi-sample VCF file. This VCF file is 99 test group SNPs and 1 control group SNPs mixed. I want only test group SNP, so i tried to many select variants method. but its still remain control SNPs. Is there any methods to know the separate control SNPs and test group SNPs? I will be happy if anybody suggest me idea regarding this. Thank you.
I understand you want to separate a large multisample VCF file into 1 column control and 99 columns with Test group SNVs ?

Can't vcflib do this for you ?

https://github.com/vcflib/vcflib#vcflib

    vcfremovesamples or vcfkeepsamples.