bcftools query missense_variant SNPs from gnomad VCF files

Question

[Shicheng Guo]

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.

[Arup Ghosh]

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

Answer 1

[finswimmer]

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

[Shicheng Guo]

Thanks finswimmer. it works.

[zx8754]

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

[Shicheng Guo]

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

[Shicheng Guo]

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

Answer 2

[Emily]

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