bcftools query missense_variant SNPs from gnomad VCF files
2
2
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2.2 years ago
Shicheng Guo ★ 8.6k

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 • 1.6k views
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1
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Can you share the header and first few lines of the file?

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7
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2.2 years ago

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

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Thanks finswimmer. it works.

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

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

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

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6
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2.2 years ago

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

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