Filter VCF file by list of sites.

Question

[selplat21]

I currently have a list of a few million sites I would like to extract from a larger VCF file. I have been using the following format:

module load bcftools tabix -R sites.list Sample.vcf.gz > Sample.subset.vcf.gz

This works, but unfortunately has been taking over a week to run. Does anyone have a faster solution?

Answer 1

[Pierre Lindenbaum]

bcftools view --threads 10 --regions-file sites.bed -O b -o samples.subset.bcf samples.vcf.gz