HaplotypeCaller throws ERROR: Stack trace on generating raw variants VCF

firasr83firasr83 New YorkPosts: 7Member
edited December 2013 in Ask the GATK team


This is in regards to a small exome capture experiment that I'd recently talked about here: http://gatkforums.broadinstitute.org/discussion/3531/bam-index-files-from-1000g-not-recognized-other-questions#latest . There are 8 experimental BAMs and 22 BAMs from 1000G supplied as inputs to HaplotypeCaller. And it quits with a code exception error at 52.1%. I've attached the relevant output. Also attached is the input files list. My OS info is:

Linux 3.2.0-56-generic #86-Ubuntu SMP x86_64 GNU/Linux

Any help would be greatly appreciated!

Thank you,

Post edited by firasr83 on


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 9,983Administrator, Dev admin

    Hi Firas,

    This looks like it might be a bug. Can you confirm that all your BAM files are validated (using Picard tools)? Also, could you please check whether this also occurs with the latest version (2.8)?

    Geraldine Van der Auwera, PhD

  • firasr83firasr83 New YorkPosts: 7Member

    Thanks for the reply @Geraldine_VdAuwera. I'll try to report back with what happens with version 2.8. I don't have the original BAM files. Just the ones that have gone through the "reduced reads" step in the pipeline. I had validated the original BAMs before with no issues but trying to validate the post-"reduced reads" BAMs throws up errors, but I guess this is normal. I can send you the verification output if required.

    Stay tuned. Thanks!

  • firasr83firasr83 New YorkPosts: 7Member

    Hi @Geraldine_VdAuwera, so I ran the same input through HaplotypeCaller, GATK version 2.8 and it again threw a NullPointerException error, but this time at 29.5%. Attached is the output.

    Please let me know what you think. Would you suggest that I give up on using HaplotypeCaller and use UnifiedGenotyper instead?


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 9,983Administrator, Dev admin

    This may be a problem of incompatibility between versions. If your bams were reduced with an older version of GATK, they should be called with the same version. More recent versions are not backwards compatible with older reduced files because the format evolved rapidly over the last few versions. UG may experience the same compatibility issues.

    I recommend doing whatever is necessary to obtain the original bams. Otherwise you'll need to downgrade to an older version of GATK, but there's no guarantee that will work, and unfortunately we can't provide support for older versions.

    Geraldine Van der Auwera, PhD

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