gnomad_toolbox.filtering.pext
Functions to filter the gnomAD pext HTs.
Module Functions
Get annotation-level pext score for a single variant from the gnomAD HT. |
Functions to filter the gnomAD pext HTs.
- gnomad_toolbox.filtering.pext.get_pext_for_variant(variant=None, contig=None, position=None, ref=None, alt=None, **kwargs)[source]
Get annotation-level pext score for a single variant from the gnomAD HT.
Note
The annotation-level pext score only sums the expression of transcripts on which a variant has a given annotation. For more information, please see https://gnomad.broadinstitute.org/help/pext.
- Parameters:
variant (
Optional[str]) – Variant string in the format “chr12-235245-A-C” or “chr12:235245:A:C”. If provided, contig, position, ref, and alt are ignored.contig (
Optional[str]) – Chromosome of the variant. Required if variant is not provided.position (
Optional[int]) – Variant position. Required if variant is not provided.ref (
Optional[str]) – Reference allele. Required if variant is not provided.alt (
Optional[str]) – Alternate allele. Required if variant is not provided.kwargs – Additional arguments to pass to _get_dataset.
- Return type:
- Returns:
Table with the single variant.