Question: How could I get population or individual specific genotypes from multi sample VCF file
gravatar for nagarsaggi
10 months ago by
nagarsaggi10 wrote:

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).

snp • 352 views
ADD COMMENTlink written 10 months ago by nagarsaggi10
gravatar for Nicolas Rosewick
10 months ago by
Belgium, Brussels
Nicolas Rosewick9.1k wrote:

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).

ADD COMMENTlink written 10 months ago by Nicolas Rosewick9.1k
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