Picking a VQSR tranche for indels
Posted in Ask the GATK team | Last updated on


Comments (1)

Hi,

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.

Thanks!

Grace


Return to top Comment on this article in the forum