Sample-level VCF filters

Question

[davidjohngreen]

Hi all,

I'm trying to apply sample-level filters on a larg VCF (200,000+ individuals) and would like to know the best available tools for this. I would like to apply similar filters to those described for the aggregated VCFs from 100K (https://cnfl.extge.co.uk/pages/viewpage.action?pageId=156601552). E.g., Sample Contamination (freemix), Ratio of SNV Het to Hom calls etc.

Any advice would be greatly appreciated.

[zx8754]

Try bcftools.