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  • GATK:Unified Genotyper Error

    Hi,

    I am using GATK unified genotyper for SNP and indel calling. My code is as follows:

    $javaPath/java -Xmx4g -jar $gatkPath/GenomeAnalysisTK.jar \
    -T UnifiedGenotyper \
    -R $humanRefSequence \
    -I "$sampleID".recal.bam \
    -B:dbsnp,vcf $humanDbsnpFile \
    -nt 8 -glm BOTH \
    -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 250 \
    -l INFO \
    -A AlleleBalance -A DepthOfCoverage -A FisherStrand \
    -log "$sampleID".GATKvariants.log -o "$sampleID".GATKvariants.raw.vcf

    However, after running few minutes it's showing the following error:

    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A USER ERROR has occurred (version 1.0.5877):
    ##### 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 wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
    ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
    ##### ERROR
    ##### ERROR MESSAGE: Unable to create BasicFeatureReader using feature file , for input source: /tmp/org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub5104773249721434217.tmp
    ##### ERROR ------------------------------------------------------------------------------------------

    I looked around and couldn't find a proper solution for it. I got stuck with for quite awhile. Can anyone please tell me what is the main reason for this error and how I can overcome it?

    Many thanks in advance.

    Regards,
    Opulcy

  • #2
    the syntax for one of your parameters seems a bit unusual, is it a typo, or is it supposed to be that way?

    -B:dbsnp,vcf

    Comment


    • #3
      The syntax looks weird because that is a very old version, and the syntax has changed since. I strongly recommend you upgrade to a more recent version, Opulcy. The old version is buggy and slow; the newer version will be faster and give you much better results.

      Comment


      • #4
        Thanks for the tips. I have upgraded to the newer version. It's running fine now.

        Comment

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