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Questions about read filters and downsampling

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
This discussion was created from comments split from: Downsampling.

Comments

  • annatannat Member

    Hi,
    We are having problems running gatk commands with read filters:

    $ java -Xmx50g -jar /software/additional/GenomeAnalysisTK-2.0-39-gd091f72/GenomeAnalysisTK.jar -T RealignerTargetCreator -I /software/additional/GenomeAnalysisTK-2.0-39-gd091f72/resources/exampleBAM.bam -R /software/additional/GenomeAnalysisTK-2.0-39-gd091f72/resources/exampleFASTA.fasta -o testGATK.intervals --read_filter UnmappedReadFilter

    ERROR ------------------------------------------------------------------------------------------
    ERROR A USER ERROR has occurred (version 2.0-39-gd091f72):
    ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
    ERROR Please do not post this error to the GATK forum
    ERROR
    ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ERROR
    ERROR MESSAGE: Could not find filter with name: UnmappedReadFilter
    ERROR ------------------------------------------------------------------------------------------

    Are there other programs etc that we need in our path?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Anna, welcome to the forum!

    When using read filters, you need to strip the Filter part of the name when passing it as an argument. So UnmappedReadFilter is passed as:

      --read_filter UnmappedRead
    

    Sorry if that is not clear in the documentation, we will add a note to clarify this usage.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    That shouldn't happen. Could you please upload a small test file to our FTP so we can try to reproduce that locally? Instructions here if needed: http://www.broadinstitute.org/gatk/guide/article?id=1894

  • jgouldjgould GouldMember ✭✭

    I uploaded walker-filters.zip. I contains 2 walkers-one in which the MappingQualityFilter is applied and one in which the MappingQualityFilter is not applied. Thanks.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Thanks for the test files, I'll have a look at them today and let you know what we find in this thread.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @jgould, I just realized you sent us the walkers themselves -- what we need is the data you were running the walkers on. Can you please upload a bam snippet that reproduces the error?

  • jgouldjgould GouldMember ✭✭

    I uploaded the to walker-filter-data.zip. Thanks.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I don't see your file in our incoming directory, can you please confirm that your upload was successful?

  • jgouldjgould GouldMember ✭✭

    I uploaded the file again-sorry I don't know what happened to the previous upload. Thanks.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Thanks @jgould, I was able to reproduce the error; not sure yet if the read filters are not getting applied or if the counts are not getting updated. We'll look into it and let you know what we find in this thread.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    OK, we found the problem -- it was indeed an issue with incrementing the counts, which wasn't being done properly. The filters were actually applied, just not reported correctly by the LocusWalker. We have a proposed fix for this which is now in code review, and should get into the nightly build within a day or two.

    Thanks for reporting this issue and contributing your test files!

  • fjrossellofjrossello Member

    Hi Geraldine,

    In regards to this issue, and as @jgould reported, I noticed that even though duplicates were accurately marked and properly identified when using PrintReads with DuplicateReads filter, both UC and HC LocusWalkers failed to report the rigth no. of reads filtered.
    I am using GATK version 2.6-5-gba531bd.
    Could you please let me know if this issue has been solved? Should I update to the nightly build?

    Thanks in advance.

    Cheers,

    Fernando

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Fernando,

    This is indeed fixed in the nightly builds, and the fix will be in release 2.7 (which is imminent).

  • fjrossellofjrossello Member

    Hi Geraldine,

    Perfect, just finished testing the latest nightly build (August 19th) and this issue has been totally fixed.
    Thanks for your support, it's great.

    Cheers,

    Fernando

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