Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.
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.
0 · ·