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.
GATKPathSpecifier 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
GATK version 4.1.3.0 built at Sat, 23 Nov 2019 16:20:54 -0500.
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