Question: Extract variants from genomic range from gnomAD GRCh38
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gravatar for j.lunger18
14 months ago by
j.lunger1810
j.lunger1810 wrote:

With the new release of gnomAD, I want to pull variants from several genes for which I have their genomic coordinates. I was successfully able to do this for gnomad GRCh37, so I'm trying to do the same with the following terminal command:

module load google-cloud-sdk
tabix -h gs://gnomad-public/release/3.0/vcf/genomes/gnomad.genomes.r3.0.sites.chr1.vcf.bgz Y:XXXX-XXXX > OUTPUTfile.vcf

While my output file has all of the gnomAD meta-data in the correct vcf format, there are no listed variants... I couldn't find any documentation on how to pull specific locations, this code was just given to me by someone else, so any help would be great.

variants gnomad exome genome • 442 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by j.lunger1810
1

It may be hard to help you without knowing Y:XXXX-XXXX

ADD REPLYlink written 14 months ago by WouterDeCoster45k

Y = chromosome, X = genomic positions --> for p53 this would be something like 17:7661779-7687550

ADD REPLYlink modified 14 months ago • written 14 months ago by j.lunger1810

I know how coordinates work, thank you very much. It doesn't hurt to be specific, as such we can replicate your problem.

ADD REPLYlink written 14 months ago by WouterDeCoster45k
1

Are you using intervals in the format chrY:XXXX-XXXX ?

The older versions of gnomAD were mapped to hg19, with chromosome names like 1,2,3,X,Y The new version 3 of gnomAD is mapped to GRCh38, with chromosome names like chr1, chr2, chrX, chrY

ADD REPLYlink written 14 months ago by rbagnall1.7k

check the chromosome notation for query and indexed vcf (chrY vs Y) ? If they match, expand the coordinates, to check if there are any variants at all at said range. @ j.lunger18

ADD REPLYlink written 14 months ago by cpad011214k
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