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FuncotatorDataSourceDownloader

Data source downloader for Funcotator.

Category Variant Evaluation and Refinement


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 current minimum of the data sources supported as defined in org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils#CURRENT_MINIMUM_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.
--germline
false Download the latest pre-packaged datasources for germline functional annotation.
--help
 -h
false display the help message
--output
 -O
null 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
null A configuration file to use with the GATK.
--QUIET
false Whether to suppress job-summary info on System.err.
--tmp-dir
null 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.


--arguments_file / NA

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

List[File]  []


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

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

boolean  false


--gatk-config-file / NA

A configuration file to use with the GATK.

String  null


--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  [ [ -∞  ∞ ] ]


--gcs-project-for-requester-pays / NA

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.

String  ""


--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


--help / -h

display the help message

boolean  false


--output / -O

Output location for the data sources.

File  null


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

Overwrite output file if it exists already.

boolean  false


--QUIET / NA

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

Boolean  false


--showHidden / -showHidden

display hidden arguments

boolean  false


--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


--tmp-dir / NA

Temp directory to use.

String  null


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

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false


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

Whether to use the JdkInflater (as opposed to IntelInflater)

boolean  false


--validate-integrity / -validate-integrity

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

boolean  false


--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


--version / NA

display the version number for this tool

boolean  false


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GATK version 4.1.0.0 built at Wed, 30 Jan 2019 10:21:04 +0530.