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bcftools query missense_variant SNPs from gnomad VCF files

Hi All,

I downloaded vcf files from gnomad , I want to filter some SNPs which are 'missense_variant' in vep annotation. 

vep=A|missense_variant|MODERATE|ABCB1|ENSG00000085563|Transcript|ENST00000265724|

However, I cannot find any effective way to filter and extract these SNPs with bcftools

bcftools view -f PASS -i 'INFO/AF[0] > 0.1 & vep{1} =="missense_variant"' gnomad.exomes.r2.1.sites.chr13.vcf.bgz

Any suggestions?

Thanks.

bcftools vep
• 4,700 views • link
updated by Emily Emily • written by Shicheng Guo Shicheng Guo

Can you share the header and first few lines of the file?

• 1 views • link
written by Arup Ghosh Arup Ghosh

2 answers

Hello Shicheng Guo ,

try this:

$ bcftools view -f PASS -i 'INFO/AF[0] > 0.1 & INFO/vep ~ "missense_variant"' gnomad.exomes.r2.1.sites.chr13.vcf.bgz

fin swimmer

• 1 views • link
written by finswimmer finswimmer

Thanks finswimmer. it works.

• 1 views • link
written by Shicheng Guo Shicheng Guo

Please consider accepting as an answer: "Thanks" == "upvote"; "it works" == "accept"

• 1 views • link
written by zx8754 zx8754

Hi Finswimmer, how to avoid multi-allelic SNPs with bcftools view or query? Thanks.

• 1 views • link
written by Shicheng Guo Shicheng Guo

It looks I find it: bcftools view -m2 -M2 -v snps gnomad.exomes.r2.1.sites.chr13.vcf.bgz

• 1 views • link
written by Shicheng Guo Shicheng Guo

You can just use the filter options that ship with the VEP.

• 1 views • link
written by Emily Emily

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