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HaplotypeCaller --fullHaplotype not outputting full haplotype

chochochocho Posts: 1Member
edited August 2012 in Ask the GATK team

I am also having a problem with HaplotypeCaller - when I set the flag to print out full haplotypes, no haplotype files are created. Here is my command:

java -jar /home/chodon/applications/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R /home/chodon/comb_eny/abyss/final_contigs/A2/Assembly.fasta -I /home/chodon/comb_eny/abyss/final_contigs/A2/bowtie2_out/A2.sorted.bam --fullHaplotype --ignoreLaneInfo -o /home/chodon/comb_eny/abyss/final_contigs/A2/GATK_haplo2.out

Any help is much appreciated! Thanks, C

Post edited by Geraldine_VdAuwera on


  • rpoplinrpoplin Posts: 122GATK Dev mod

    Hi there,

    The --fullHaplotype option is an experimental and unsupported command line argument for the HaplotypeCaller. In version 2.1 this will be reflected as an "Advanced" option in the documentation.

    However, if you are willing to experiment with this you need to add --genotypeFullActiveRegion to your command line and run it again. I would be very curious to hear what you think of how the output is formatted and if you find the argument useful at all.


  • chochochocho Posts: 1Member

    Hi, Thanks for your quick reply!

    When I added --genotypeFullActiveRegion, full command here:

    java -jar /home/chodon/applications/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R /home/chodon/comb_eny/abyss/final_contigs/A2/Assembly.fasta -I /home/chodon/comb_eny/abyss/final_contigs/A2/bowtie2_out/A2.sorted.bam --genotypeFullActiveRegion --fullHaplotype --ignoreLaneInfo -o /home/chodon/comb_eny/abyss/final_contigs/A2/GATK_haplo3.out

    I got an error message: Code exception - here is the stack trace

    ERROR stack trace

    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.callWalkerMapOnActiveRegions(
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(
    at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
    at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(

    Thanks again!

  • rpoplinrpoplin Posts: 122GATK Dev mod

    Ah, I see what the problem is but unfortunately you'll have to wait until we release version 2.1 (targeted for next week) to get the fix. Thanks for letting me know that someone is interested in this command line option though!

  • sbrubakersbrubaker Posts: 4Member

    Hi, I am trying the same things, and I have version 2.1. I get an error that says "Unexpected bases in allele bases"

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,781Administrator, GATK Dev admin

    Hi @sbrubaker, have you tried validating your bam file? That type of error is often associated with invalid bams.

    Geraldine Van der Auwera, PhD

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