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Overlapping INDEL calls

lpryszczlpryszcz Member Posts: 3

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

Best Answer

Answers

  • lpryszczlpryszcz Member Posts: 3

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

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