Question: bcftools query missense_variant SNPs from gnomad VCF files
2
gravatar for Shicheng Guo
7 weeks ago by
Shicheng Guo7.4k
Shicheng Guo7.4k wrote:

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.

vep bcftools • 219 views
ADD COMMENTlink modified 7 weeks ago by Emily_Ensembl17k • written 7 weeks ago by Shicheng Guo7.4k
1

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

ADD REPLYlink written 7 weeks ago by arup870
6
gravatar for finswimmer
7 weeks ago by
finswimmer11k
Germany
finswimmer11k wrote:

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

ADD COMMENTlink written 7 weeks ago by finswimmer11k

Thanks finswimmer. it works.

ADD REPLYlink written 7 weeks ago by Shicheng Guo7.4k

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

ADD REPLYlink written 7 weeks ago by zx87546.8k

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

ADD REPLYlink written 7 weeks ago by Shicheng Guo7.4k

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

ADD REPLYlink written 7 weeks ago by Shicheng Guo7.4k
5
gravatar for Emily_Ensembl
7 weeks ago by
Emily_Ensembl17k
EMBL-EBI
Emily_Ensembl17k wrote:

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

ADD COMMENTlink written 7 weeks ago by Emily_Ensembl17k
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