GATK HaplotypeCaller Error: Java stack error

gracecgracec United StatesMember

I get the same error repetitively while running GATK HaplotypeCaller (see below). This seems to occur around the same chromosome positions for each of the 3 bam samples. Rest of the samples run without error.

I am running it on GATK v 3.6 and the latest Java version (8u66). I have tried running it on gatk/3.6-nightly-2016-08-01-g4a102f4 as well.

Any suggestions would be most welcome!

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