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MalformedReadFilter walker not found in GATK?

Hi GATK Team,

Sorry, this is probably a naive question. I would like to use the MalformedReadFilter walker, but downloading the latest GATK release and following the documentation at (https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_engine_filters_MalformedReadFilter.php):

I used this command,
java -jar /Downloads/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T MalformedReadFilter

But I am getting this error:

ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: MalformedReadFilter

Is there an error in syntax?

Thanks a lot,
Steve

Best Answer

Answers

  • newGATKusernewGATKuser CaseMember

    Thanks @Geraldine_VdAuwera , that makes a lot of sense.

  • samnichollssamnicholls Wales, UKMember

    @Geraldine_VdAuwera said:
    Well, read filters are essentially options that are added to analysis tools. So if you wanted to apply a read filter to your data, you could for example run the PrintReads tools (which at its most basic just reads in a bam and writes out the contents to a new bam) with the read filter added, like this:

    java -jar GenomeAnalysisTK.jar -R genome_ref.fasta -T PrintReads -rf MalformedRead -I input.bam -o output.bam
    

    Note that the filter name gets stripped of the "Read" part.

    @Geraldine_VdAuwera
    It turns out that using -rf MalformedRead when using the PrintReads tool causes an error of its own. It seems that because PrintReads actually applies the MalformedReadFilter automatically, that the additional -rf MalformedRead causes a duplicate definition error:

    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR stack trace 
    org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Duplicate definition of argument with full name: filter_reads_with_N_cigar
            at org.broadinstitute.gatk.utils.commandline.ArgumentDefinitions.add(ArgumentDefinitions.java:59)
            at org.broadinstitute.gatk.utils.commandline.ParsingEngine.addArgumentSource(ParsingEngine.java:150)
            at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:207)
            at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
            at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
    ##### ERROR
    ##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
    ##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
    ##### ERROR Visit our website and forum for extensive documentation and answers to 
    ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ##### ERROR
    ##### ERROR MESSAGE: Duplicate definition of argument with full name: filter_reads_with_N_cigar
    ##### ERROR ------------------------------------------------------------------------------------------
    
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Yep, this has been pointed out; it's an annoying quirk (you could even call it a bug) of the engine/parser. Instead of recognizing that nothing needs to be done, it freaks out because the thing is already sitting in the slot that it's trying to put the thing in. Not to be too technical about it :)

    It's one of those things that we've just never got around to fixing because it involves some unnecessarily complicated code, so would be more work than it's really worth. (I say that hoping you didn't spend hours tearing your hair out because of this).

  • samnichollssamnicholls Wales, UKMember

    @Geraldine_VdAuwera said:
    Yep, this has been pointed out;

    Aha! I thought I would just post it here in case anybody has the same problem following the example in future.

    it's an annoying quirk (you could even call it a bug)

    I think I prefer quirk :)

    It's one of those things that we've just never got around to fixing because it involves some unnecessarily complicated code, so would be more work than it's really worth. (I say that hoping you didn't spend hours tearing your hair out because of this).

    I know that feeling, no worries! And not this time, phew!

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