How to retrieve LoF and missense variants in WES data?

Question

[_quantum_girl_]

I don't believe plink can do this, any idea of how to filter variants to retrieve only missense and LoF? I have several file formats: bgen, vcf and plink. I can use whichever.

Answer 1

[Pierre Lindenbaum]

for example annotate the vcf with snpEff, then filter with snpSift http://pcingola.github.io/SnpEff/

Answer 2

[luffy]

@ _quantum_girl_, as Pierre mentioned, you can annotate your VCF with snpEff or ensembl vep once you annotated you could filter null and missense variants using a smiple code with R/python. while you are annotating keep the output format as tab delimited file.