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GATK Module help command does not work?

SkyWarriorSkyWarrior TurkeyMember ✭✭✭


As usual I like checking the help blobs from the original application itself but it seems to be broken for GATK

gatk HaplotypeCaller -h throws exception.

Gokalps-Mac-mini:~ sky$ gatk HaplotypeCaller -h
Using GATK jar /Users/sky/scripts/gatk-package-
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Users/sky/scripts/gatk-package- HaplotypeCaller -h
java.lang.IllegalArgumentException: Allowed values request for unrecognized string argument: input
    at org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor.getAllowedValuesForDescriptorHelp(
    at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.usageForPluginDescriptorArgumentIfApplicable(
    at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.makeArgumentDescription(
    at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.printArgumentUsage(
    at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.lambda$printArgumentUsageBlock$2(
    at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.printArgumentUsageBlock(
    at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.usage(
    at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.parseArguments(
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.parseArgs(
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(
    at org.broadinstitute.hellbender.Main.mainEntry(
    at org.broadinstitute.hellbender.Main.main(

And this is what happens in

Using GATK jar /gatk/build/libs/gatk-package-
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/build/libs/gatk-package- HaplotypeCaller -h
USAGE: HaplotypeCaller [arguments]

Call germline SNPs and indels via local re-assembly of haplotypes

Required Arguments:

--input,-I:String             BAM/SAM/CRAM file containing reads  This argument must be specified at least once.

--output,-O:String            File to which variants should be written  Required.

--reference,-R:String         Reference sequence file  Required.

Optional Arguments:

--activity-profile-out:String Output the raw activity profile results in IGV format  Default value: null.

                              If true, adds a PG tag to created SAM/BAM/CRAM files.  Default value: true. Possible
                              values: {true, false}

                              If true, adds a command line header line to created VCF files.  Default value: true.
                              Possible values: {true, false}

--alleles:FeatureInput        The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES
                              Default value: null.

                              If provided, we will annotate records with the number of alternate alleles that were
                              discovered (but not necessarily genotyped) at a given site  Default value: false. Possible
                              values: {true, false}

Same problem persists in docker version as well.


Best Answer


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