Any known problems with IndelRealigner code in gsa-stable?

evolvedmicrobeevolvedmicrobe MGHPosts: 14Member

Does anyone know of any known issues with the indelrealigner? The GATK is calling 1000s of SNPs on one genome I have due to bad realignments. It appears the target finder identifies regions of the genome that are essentially perfectly aligned, but when the realigner gets to these areas it remits the reads as a new alignment that is a train-wreck compared to what the re-aligner started with. Am going to investigate further but thought I would check if this rings any bells. I am using the flag -model USE_READS and have no known indels to work with.

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  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,973Administrator, GATK Developer admin

    Hi there,

    IndelRealigner is a mature tool and as far as we no there are no outstanding issues. Have you checked that your reference is ok and matches your bam files?

    Geraldine Van der Auwera, PhD

  • evolvedmicrobeevolvedmicrobe MGHPosts: 14Member

    Yep, issue doesn't seem to be the reference. Unfortunately I can't reproduce the error too easily as if I only extract the region of the genome that appears to be problematic, the indel realigner then works fine on the smaller dataset. Will keep looking...

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