Data source downloader for Funcotator.

Category Variant Evaluation and Refinement

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Overview

FuncotatorDataSourceDownloader is a tool to download the latest data sources for Funcotator.

General Information

This tool can download pre-packaged data sources for both the somatic and germline use cases. The data sources downloaded by this tool correspond to the latest / current maximum of the data sources supported as defined in org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils#CURRENT_MAXIMUM_DATA_SOURCE_VERSION.

To download and extract the data sources, you can invoke FuncotatorDataSourceDownloader in the following ways:

• For somatic data sources:
  

   ./gatk FuncotatorDataSourceDownloader --somatic --validate-integrity --extract-after-download

• For germline data sources:
  

   ./gatk FuncotatorDataSourceDownloader --germline --validate-integrity --extract-after-download

Notes

• By default FuncotatorDataSourceDownloader will not overwrite data sources if they already exist locally.
• It is recommended to run the validation step after downloading the data sources to ensure download integrity.
• Using this tool will result in longer download times for data sources than if gsutil were invoked directly to copy down the data sources.
  This is a known issue and is due to the tool printing the progress of the download.

FuncotatorDataSourceDownloader specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s)	Default value	Summary
Optional Tool Arguments
--arguments_file		read one or more arguments files and add them to the command line
--extract-after-download	false	Extract the data sources to a sibling folder after they have been downloaded.
--gcs-max-retries  -gcs-retries	20	If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--gcs-project-for-requester-pays		Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.
--germline	false	Download the latest pre-packaged datasources for germline functional annotation.
--help  -h	false	display the help message
--output  -O		Output location for the data sources.
--overwrite-output-file	false	Overwrite output file if it exists already.
--somatic	false	Download the latest pre-packaged datasources for somatic functional annotation.
--validate-integrity	false	Validate the integrity of the data sources after downloading them using sha256.
--version	false	display the version number for this tool
Optional Common Arguments
--gatk-config-file		A configuration file to use with the GATK.
--QUIET	false	Whether to suppress job-summary info on System.err.
--tmp-dir		Temp directory to use.
--use-jdk-deflater  -jdk-deflater	false	Whether to use the JdkDeflater (as opposed to IntelDeflater)
--use-jdk-inflater  -jdk-inflater	false	Whether to use the JdkInflater (as opposed to IntelInflater)
--verbosity	INFO	Control verbosity of logging.
Advanced Arguments
--showHidden	false	display hidden arguments

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

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--arguments_file

read one or more arguments files and add them to the command line

List[File]  []

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--extract-after-download / -extract-after-download

Extract the data sources to a sibling folder after they have been downloaded.

boolean  false

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--gatk-config-file

A configuration file to use with the GATK.

String  null

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--gcs-max-retries / -gcs-retries

If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection

int  20  [ [ -∞  ∞ ] ]

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--gcs-project-for-requester-pays

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.

String  ""

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--germline / -germline

Download the latest pre-packaged datasources for germline functional annotation.

Exclusion: This argument cannot be used at the same time as somatic, testing-override-path-for-datasources-sha256, testing-override-path-for-datasources.

boolean  false

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--help / -h

display the help message

boolean  false

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--output / -O

Output location for the data sources.

File  null

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--overwrite-output-file / -overwrite-output-file

Overwrite output file if it exists already.

boolean  false

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--QUIET

Whether to suppress job-summary info on System.err.

Boolean  false

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--somatic / -somatic

Download the latest pre-packaged datasources for somatic functional annotation.

Exclusion: This argument cannot be used at the same time as germline, testing-override-path-for-datasources-sha256, testing-override-path-for-datasources.

boolean  false

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--tmp-dir

Temp directory to use.

GATKPath  null

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--use-jdk-deflater / -jdk-deflater

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false

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--use-jdk-inflater / -jdk-inflater

Whether to use the JdkInflater (as opposed to IntelInflater)

boolean  false

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--validate-integrity / -validate-integrity

Validate the integrity of the data sources after downloading them using sha256.

boolean  false

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--verbosity / -verbosity

Control verbosity of logging.

The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:

ERROR

WARNING

INFO

DEBUG

LogLevel  INFO

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--version

display the version number for this tool

boolean  false

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GATK version 4.3.0.0 built at Wed, 12 Oct 2022 21:04:44 -0400.