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HaplotypeCaller throws ERROR: Stack trace on generating raw variants VCF

New YorkMember
edited December 2013

Hello,

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,
Firas

Tagged:

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)?

• New YorkMember

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!

• New YorkMember

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?

Thanks,
Firas