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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

There are 2 comments on this article. To see them or add your own, view this post on the forum