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expected tranch plot?

burcuburcu GermanyMember

Dear GATK team,

Very recently I ran a batch of 80 Exome datasets. When I checked the VQSR tranches plot, I noticed that any false positives or negatives were indicated. I am sending you the plot in the attachment. If my datasets are really lack of false positives or negatives, this would be amazing :-), however I do not think so. If you could let me know what is the underlying reason of this issue, I would be grateful.

Best regards,
Burcuimageimage

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I'm not sure but here's a thought. The tool estimates the amount of false positives using the TiTv ratio of novel sites as a proxy, which is an imperfect approach as it involves a few assumptions that are not guaranteed. You might have very high TiTv because of the regions of the genome you're looking at, or your organism if it's non-human data. This would cause the tool to underestimate false positives.

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