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.

Picking a VQSR tranche for indels

gtiaogtiao Cambridge, MAPosts: 6Member


Given that there's no tranche plot generated for indels using VariantRecalibrator, how do we assess which tranche to pick for the next step, ApplyRecalibration? On SNP mode, I'm using tranche plots to evaluate the tradeoff between true and false positive rates at various tranche levels, but that's not possible with indels.




  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,235Administrator, GSA Member admin

    Hi Grace,

    That's a good question. For indels you'll need to do some more analysis yourself to determine which tranche to pick. One thing you can do is generate separate files for each tranche, then compare them in VariantEval. For example, look at the proportion of known vs novel in each.

    Geraldine Van der Auwera, PhD

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