gnomad_qc.v4.annotations.vep_context_ht

Script to add VEP annotations to the GRCh38 context Table.

usage: gnomad_qc.v4.annotations.vep_context_ht.py [-h]
                                                  [--input-context-ht-vep-version]
                                                  [--vep-version] [--test]
                                                  [--slack-channel SLACK_CHANNEL]
                                                  [--overwrite]

Named Arguments

--input-context-ht-vep-version

Version of VEPed context Table to annotate onto. Drops ‘vep’ and ‘vep_proc_id’ annotations before re-annotating.

Default: “101”

--vep-version

Version of VEP the context Table is being annotated with.

Default: “105”

--test

Runs a test on two partitions of the MT.

Default: False

--slack-channel

Slack channel to post results and notifications to.

--overwrite

Overwrite data if it exists.

Default: False

Module Functions

`gnomad_qc.v4.annotations.vep_context_ht.main`(args)	Add VEP annotations to the GRCh38 context Table.
`gnomad_qc.v4.annotations.vep_context_ht.get_script_argument_parser`()	Get script argument parser.

Script to add VEP annotations to the GRCh38 context Table.

gnomad_qc.v4.annotations.vep_context_ht.main(args)[source]: Add VEP annotations to the GRCh38 context Table.