Extract variants from genomic range from gnomAD GRCh38

Question

[j.lunger18]

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.

[WouterDeCoster]

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

[j.lunger18]

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

[WouterDeCoster]

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

[rbagnall]

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

[cpad0112]

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

Answer 1

[Kalin]

I created a python package based on SQLite databases, where you can easily query all gnomAD variants for GRCh37/38. https://github.com/KalinNonchev/gnomAD_DB I have precomputed SQLite databases for gnomAD WGS for GRCh37/38 in the description of the package. Please take a look there.