gnomad_qc.v4.create_release.create_de_novo_release

Script to create release de novo HT for v4 exomes.

usage: gnomad_qc.v4.create_release.create_de_novo_release.py
       [-h] [--overwrite] [-t] [--n_partitions N_PARTITIONS]
       [--generate-de-novo-calls] [--generate-final-ht] [--generate-final-tsv]
       [--slack-channel SLACK_CHANNEL]

Named Arguments

--overwrite

Overwrite data

Default: False

-t, --test

Runs a test on chr20

Default: False

--n_partitions

Number of partitions to use for the output Table.

Default: 1000

--generate-de-novo-calls

Generate de novo calls HT.

Default: False

--generate-final-ht

Generate the final HT for de novo release.

Default: False

--generate-final-tsv

Generate the final TSV for de novo release.

Default: False

--slack-channel

Slack channel to post results and notifications to.

Module Functions

`gnomad_qc.v4.create_release.create_de_novo_release.get_releasable_de_novo_calls_ht`(mt, ...)	Get de novo calls Hail Table.
`gnomad_qc.v4.create_release.create_de_novo_release.aggregate_and_annotate_de_novos`(ht)	Aggregate and annotate de novo calls.
`gnomad_qc.v4.create_release.create_de_novo_release.restructure_for_tsv`(ht)	Restructure the de novo release HT for TSV export.
`gnomad_qc.v4.create_release.create_de_novo_release.main`(args)	Create de novo release ht.
`gnomad_qc.v4.create_release.create_de_novo_release.get_script_argument_parser`()	Get script argument parser.

Script to create release de novo HT for v4 exomes.

gnomad_qc.v4.create_release.create_de_novo_release.get_releasable_de_novo_calls_ht(mt, priors_ht, ped, test=False, n_partitions=1000)[source]

Get de novo calls Hail Table.

Parameters:

mt (MatrixTable) – Dense MatrixTable of the releasable trios.
priors_ht (Table) – Table with AFs used as population frequency priors in de novo calculations.
ped (Pedigree) – Pedigree.
test (bool) – Whether to filter to chr20 for testing. Default is False.
n_partitions (int) – Number of partitions to use for the output Table. Default is 1000.

Return type:

Table

Returns:

Hail Table with de novo calls.

gnomad_qc.v4.create_release.create_de_novo_release.aggregate_and_annotate_de_novos(ht)[source]

Aggregate and annotate de novo calls.

This step produces high quality coding de novos for release. High quality is defined as variants that:

Are not in low-confidence regions
Do not have a * alt allele
Passed variant QC
Have either HIGH (all probabilities) or MEDIUM (P-value >=0.9) confidence of being a de novo
Have a coding consequence
Pass gnomAD v4.1 exomes allele frequency (AF) and callset allele count (AC) filters

Parameters:: ht (Table) – De novo calls Table.
Return type:: Table
Returns:: Aggregated and annotated Table.

gnomad_qc.v4.create_release.create_de_novo_release.restructure_for_tsv(ht)[source]

Restructure the de novo release HT for TSV export.

Note

This function will only be used for the TSV of high-quality coding de novos.

Parameters:: ht (Table) – De novo release HT.
Return type:: Table
Returns:: Restructured HT.

gnomad_qc.v4.create_release.create_de_novo_release.main(args)[source]: Create de novo release ht.