GATK HaplotypeCaller Error: Java stack error
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!