How could I get population or individual specific genotypes from multi sample VCF file

Question

[nagarsaggi]

I build a neighbour-joining tree from a multi-sample (genotype) vcf file and could see the population structure in the samples. I was wondering if I could extract population-specific variant/genotype information from vcf file (present in one population but absent in other).

Answer 1

[Nicolas Rosewick]

so you want to extract GT from subsets of samples from your VCF ? If yes use bcftools view -S sample_list.txt input.vcf > subset.vcf where sample_list.txt is a text file containing the list of sample id you want to extract (one sample id per line).