gnomad_qc.v4.create_release.create_false_dup_liftover
Script to create custom liftover file for three false dup genes CBS, KCNE1, and CRYAA.
Module Functions
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Read in gnomAD v2 liftover table, filter to genes of interest, and return the Table. |
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Write merged v2 exomes and genomes liftover table with joint information for three clinically relevant genes. |
Script to create custom liftover file for three false dup genes CBS, KCNE1, and CRYAA.
- gnomad_qc.v4.create_release.create_false_dup_liftover.filter_liftover_to_false_dups(data_type)[source]
Read in gnomAD v2 liftover table, filter to genes of interest, and return the Table.
- Parameters:
data_type (
str) – Data type ‘exomes’ or ‘genomes’. Default is ‘exomes’.- Return type:
- Returns:
Filtered Hail Table.
- gnomad_qc.v4.create_release.create_false_dup_liftover.main(args)[source]
Write merged v2 exomes and genomes liftover table with joint information for three clinically relevant genes.
There are three clinically relevant genes impacted by false duplications in the GRCh38 reference (KCNE1, CBS, and CRYAA). To make it easier for our users to switch to gnomAD v4 and the new reference build, this script creates a new release file that combines information from the v2 exomes and genomes only for these three genes. To create this file, filter the v2 liftover files (https://gnomad.broadinstitute.org/downloads#v2-liftover) to these genes, and then merge frequency information across the exomes and genomes