Hello!
I'm pretty new to this so pardon me if this is formatted incorrectly or I'm missing something obvious.
It looks like I have the same problem as: http://gatkforums.broadinstitute.org/gatk/discussion/2319/haplotypecaller-incorrectly-making-heterozygous-calls-again but their problems seemed to be fixed simply by updating, and I'm using the current version of GATK (3.5.0). Any idea what I can do to fix this?
When processing this, I mostly used the GATK Best Practices. However, I did use joint calling instead of the mixed method, since I figured with only 93 samples, for a handful of genes, it wouldn't benefit too heavily from more efficient computation, and plugging the whole BAM in at once seemed easier.
Here's a shot from IGV of a portion of one of my samples. The circled SNPs are the ones in question. For all 3, all of the reads in the BAM are for the alternate, but the VCF produced by HaplotypeCaller has them as heterozygous (and passing filters). It seems to be pretty consistent in which SNPs it messes up. On the other hand, some samples are fine, and some are not, but I don't see a pattern as to why some work and some don't. I'd be happy to provide any other information that would help resolve this.
Thank you for any help you can provide,
Jessica Patnode
