HaplotypeCaller throws ERROR: Stack trace on generating raw variants VCF
Posted in Ask the GATK team | Last updated on 2013-12-16 03:57:51

Comments (4)


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

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