How can I get a common variant of three samples from multi-sample VCF after joint genotyping?
Hi. I’m studying about sequencing data analysis followed GATK Best practices for Germline SNP & Indel Discovery. Through the series of analysis, finally I get multi-sample VCF file from joint genotyping. After this, I want to get common variants from only three sample. I’ve conducted “Select variant” and using “—sample_name” argument and i get has three sample from vcf file. but this VCF file has not three sample variants, it contains all variant from multi-sample. so I want ask you any methods to get the common variants of three samples from multi-sample. Thank you