Overlapping INDEL calls

lpryszcz

Hi,

I have noticed, sometimes GATK UnifiedGenotyper calls overlapping INDELs even though there should be 3 non-overlapping (independent) calls.

I have attached 200bp region from my BAM, reference and vcf file, so you can reproduce this issue.

Cheers, Leszek

Geraldine_VdAuwera

Hi Leszek,

Unfortunately we can't fix this in the UnifiedGenotyper because we have stopped developing that tool in order to focus on the HaplotypeCaller. If this is a big issue for you then I suggest you use the HaplotypeCaller to call variants. Sorry for the inconvenience...

Good luck!

lpryszcz

Thanks Geraldine. I'll give it a try. L.