Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.
Intervals specified using vcf files are off by 1
I tried specifying intervals using a vcf file to HaplotypeCaller and I'm not getting the appropriate hits, because it appears that GATK is interpreting the vcf file as 0-based.
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