Is it possible to query column of particular sample on VCF?

Question

[optimistsso4co3]

I would like to extract specific samples from vcf with speed of bcftools query. Is it possible? Here is an example that obviously does not work:

bcftools query -f '%CHROM %POS %Sample1 %Sample2'

Answer 1

[Pierre Lindenbaum]

bcftools view --samples S1,S2 in.vcf

[optimistsso4co3]

Bcftools view appears to be very slow for extracting individual samples, e.g. for my 70 gigabit vcf it takes 1.5h to extract one sample.

[Pierre Lindenbaum]

split per regions, run in parallel, run bcftools concat at the end.

[optimistsso4co3]

I this case 70 segmets of 600 samples would mean 42 000 jobs, which seems risky. But i will try.

[Pierre Lindenbaum]

uh ? these are only 70 jobs (70x extract two samples) , unless I didn't understand your question.

[optimistsso4co3]

I didn't frame the problem correctly. The goal is to make individual VCF for each sample, of which there are 600 which is extremely slow with bcftools view.

I figured i could accomplish my aim with bcftools query and then substract genotypes that are present in my target sample. However, i don't know how to do that.

I will reframe the question and make another post.

Answer 2

[optimistsso4co3]

I found a viable solution using bcftools +split plugin, e.g.:

bcftools +split file.vcf -Oz -o testDir -i'GT="alt"'