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] [-v VERSION] [-t] [--generate-dense-mt]
       [--de-novo-n-partitions DE_NOVO_N_PARTITIONS] [--generate-final-ht]
       [-j TABLES_FOR_JOIN [TABLES_FOR_JOIN ...]]
       [--n-partitions N_PARTITIONS] [--generate-final-tsv]
       [--slack-channel SLACK_CHANNEL]

Named Arguments

--overwrite

Overwrite data

Default: False

-v, --version

The version of gnomAD.

Default: “4.1”

-t, --test

Runs a test on chr20

Default: False

--generate-dense-mt

Generate a dense MT for releasable trios with the de novo variants.

Default: False

--de-novo-n-partitions

Number of partitions to naive coalesce the de novo dense MT to.

Default: 100

--generate-final-ht

Generate the final HT for de novo release.

Default: False

-j, --tables-for-join

Tables to join for release

Default: [‘de_novos’, ‘dbsnp’, ‘filters’, ‘info’, ‘in_silico’, ‘vep’, ‘joint_freq’, ‘exomes_an’]

--n-partitions

Number of partitions to naive coalesce the release Table to.

Default: 100

--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.filter_de_novos`(ht)	Filter the trio stats Table to de novo variants.
`gnomad_qc.v4.create_release.create_de_novo_release.get_releasable_trios_dense_mt`(...)	Densify the VDS to only the releasable trios.
`gnomad_qc.v4.create_release.create_de_novo_release.custom_de_novo_select`(ht, **_)	Select fields from de novo stats Table.
`gnomad_qc.v4.create_release.create_de_novo_release.custom_joint_freq_select`(ht, **_)	Select joint freq fields for release.
`gnomad_qc.v4.create_release.create_de_novo_release.custom_joint_freq_select_globals`(ht)	Select joint freq globals for release.
`gnomad_qc.v4.create_release.create_de_novo_release.custom_info_select`(ht, **_)	Select fields for info Hail Table annotation in de novo release.
`gnomad_qc.v4.create_release.create_de_novo_release.custom_an_select`(ht, **_)	Select AN for release.
`gnomad_qc.v4.create_release.create_de_novo_release.custom_an_select_globals`(ht)	Select AN Table globals for release.
`gnomad_qc.v4.create_release.create_de_novo_release.get_de_novo_config`()	Get de novo release config.
`gnomad_qc.v4.create_release.create_de_novo_release.get_de_novo_release_ht`(...)	Get de novo release HT.
`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.filter_de_novos(ht)[source]

Filter the trio stats Table to de novo variants.

Removes variants that are not de novo, AS_lowqual, and ‘*’ alleles.

Parameters:: ht (Table) – Trio stats Table.
Return type:: Table
Returns:: Filtered Table.

gnomad_qc.v4.create_release.create_de_novo_release.get_releasable_trios_dense_mt(fam_ht, var_ht, test=False)[source]

Densify the VDS to only the releasable trios.

Parameters:

fam_ht (Table) – Table containing family information.
var_ht (Table) – Table containing trio stats.
test (bool) – Whether to filter to chr20 for testing. Default is False.

Return type:

Returns:

Dense MatrixTable with de novo variants in releasable trios.

gnomad_qc.v4.create_release.create_de_novo_release.custom_de_novo_select(ht, **_)[source]: Select fields from de novo stats Table.

gnomad_qc.v4.create_release.create_de_novo_release.custom_joint_freq_select(ht, **_)[source]

Select joint freq fields for release.

Parameters:: ht (Table) – Joint freq Hail Table.
Return type:: Dict[str, Expression]
Returns:: Select expression dict.

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

Select joint freq globals for release.

Parameters:: ht (Table) – Joint freq Hail Table.
Return type:: Dict[str, Expression]
Returns:: Select expression dict

gnomad_qc.v4.create_release.create_de_novo_release.custom_info_select(ht, **_)[source]

Select fields for info Hail Table annotation in de novo release.

Parameters:: ht (Table) – Info Hail Table.
Return type:: Dict[str, Expression]
Returns:: Select expression dict.

gnomad_qc.v4.create_release.create_de_novo_release.custom_an_select(ht, **_)[source]

Select AN for release.

Parameters:: ht (Table) – Hail Table with AN.
Return type:: Dict[str, Expression]
Returns:: Select expression dict.

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

Select AN Table globals for release.

Parameters:: ht (Table) – Hail Table with AN.
Return type:: Dict[str, Expression]
Returns:: Select expression dict.

gnomad_qc.v4.create_release.create_de_novo_release.get_de_novo_config()[source]

Get de novo release config.

Return type:: Dict[str, dict]
Returns:: Config dict.

gnomad_qc.v4.create_release.create_de_novo_release.get_de_novo_release_ht(tables_for_join, version, test=False)[source]

Get de novo release HT.

Parameters:

tables_for_join (list[str]) – Tables to join for release.
version (str) – Version of gnomAD.
test (bool) – Run test on chr20. Default is False.

Return type:

Table

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

Restructure the de novo release HT for TSV export.

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.