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How to retrieve LoF and missense variants in WES data?

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.

bcftools variants plink snps
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updated by luffy • luffy • written by _quantum_girl_ • _quantum_girl_

2 answers

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

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written by Pierre Lindenbaum Pierre Lindenbaum

@ _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.

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written by luffy • luffy

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