Problem understanding construction of Tranches Plots
I must be missing a fundamental concept about VQSR, because I cannot figure out how false positives are defined in the construction of the tranches plot.
First, I understand a tranche as a subset of the original raw sites, in which sites PASS if they are above a particular VQSLOD score that allows to keep N% of the sites in the truth set. From this, all sites in the tranche must have FILTER=PASS, and some of those sites will be novel because they do not appear in any of the resources provided.
When constructing the tranches plot, only novel sites are considered.
So, if in order to be in the tranche, a site must have PASSed filtering by VQSLOD score, then where do the tranche specific false positives come from?
This question is derived from a previous post where it was indicated that
All the SNPs that are found are considered "positives" because they were found by earlier stages of analysis. "True" vs "False" positives is simply referring to whether they pass the VQSR filter in a given tranche.
Is there a stage in the analysis that I am not considering?