gnomad_qc.analyses.compute_pext

Script to get release pext annotation files.

Module Functions

gnomad_qc.analyses.compute_pext.filter_to_test(ht, ...)

Filter ht and tx_mt to a test set of genes.

gnomad_qc.analyses.compute_pext.get_pipeline_resources(...)

Get pipeline resources for pext annotation pipeline.

gnomad_qc.analyses.compute_pext.main(args)

Script to get release pext annotation files.

Script to get release pext annotation files.

gnomad_qc.analyses.compute_pext.filter_to_test(ht, tx_mt)[source]

Filter ht and tx_mt to a test set of genes.

Genes to filter to:

  • APOE

  • HTR2A

  • C1orf170/PERM1

  • TNFRSF25

  • TNFRSF18

Parameters:

  • ht (Table) – VEP context HT to filter.

  • tx_mt (MatrixTable) – Transcript MT to filter.

Return type:

Tuple[Table, MatrixTable]

Returns:

Filtered HT and MT.

gnomad_qc.analyses.compute_pext.get_pipeline_resources(test, gtex_version, overwrite)[source]

Get pipeline resources for pext annotation pipeline.

Parameters:

  • test (bool) – Whether to get resources for a test run.

  • gtex_version (str) – GTEx version to get resources for. Must be one of ‘v7’ or ‘v10’.

  • overwrite (bool) – Whether to overwrite existing data.

Return type:

PipelineResourceCollection

Returns:

Pipeline resource collection for pext annotation pipeline.

gnomad_qc.analyses.compute_pext.main(args)[source]

Script to get release pext annotation files.