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.

Overlapping INDEL calls

lpryszczlpryszcz Posts: 3Member

Hi,

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

image

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

Cheers, Leszek

tgz
tgz
test.tgz
134K
test.igv.png
1680 x 893 - 28K

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