gnomad_toolbox.filtering.constraint

Functions to filter gnomAD sites HT by constraint metrics.

Module Functions

gnomad_toolbox.filtering.constraint.get_observed_plofs_for_gene_constraint(...)

Filter to observed pLoF variants used for gene constraint metrics.

Functions to filter gnomAD sites HT by constraint metrics.

gnomad_toolbox.filtering.constraint.get_observed_plofs_for_gene_constraint(gene_symbol, version=None, variant_ht=None, coverage_ht=None)[source]

Filter to observed pLoF variants used for gene constraint metrics.

The pLOF variant count displayed on the browser meets the following requirements:

  • PASS variant QC

  • SNV

  • Allele frequency ≤ 0.1%

  • High-confidence LOFTEE in the MANE Select or Canonical transcript

  • ≥ a specified coverage threshold (depends on the version)

Parameters:

  • gene_symbol (str) – Gene symbol.

  • version (str) – Optional gnomAD dataset version. If not provided, uses the gnomAD session version.

  • variant_ht (Table) – Optional Hail Table with variants. If not provided, uses the exome variant Table for the gnomAD session version.

  • coverage_ht (Table) – Optional Hail Table with coverage data. If not provided, uses the exome coverage Table for the gnomAD session version.

Return type:

Table

Returns:

Table with pLoF variants.