Tool:Query and annotate variants with gnomAD python
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18 months ago
Kalin ▴ 50

Hello,

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. You could query the exon intervals of the genes using it.

This package scales the huge gnomAD files (on average ~120G/chrom) to a SQLite database with a size of 34G for WGS v2.1.1 (261.942.336 variants) and 98G for WGS v3.1.2 (about 759.302.267 variants), and allows scientists to look for various variant annotations present in gnomAD (i.e. Allele Count, Depth, Minor Allele Frequency, etc. - here you can find all selected features given the genome version). (A query containing 300.000 variants takes ~40s.)

It extracts from a gnomAD vcf about 23 variant annotations. You can find further infromation about the exact fields here.

<h5>The package works for all currently available gnomAD releases.(July 2022)</h5>
sql disease variants python gnomad • 841 views
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