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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


Best Answers


  • 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!

  • 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: 10,557Administrator, 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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