expected tranch plot?
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.