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Help choosing truth sensitivity
I am trying to decide which set of SNPs to use for my downstream analyses. I need to have > 1SNP per Kbp to detect signatures of selection (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4611237/). The tranches that achieve this SNP density start from 80% truth sensitivity.
Looking at the tranches plot , tranches 80-90 are reasonable based on the novel TiTv ratio for the species I am working with.
However, the fraction of false positives (Target TiTv ratio = 2) might be too high for these tranches (0.2-0.25):
| targetSensitivity| nTP| nFP| FP_fraction| |-----------------:|-------:|-------:|-----------:| | 60| 140491| 5357| 0.037| | 65| 200758| 10581| 0.050| | 70| 289547| 23544| 0.075| | 75| 303540| 76741| 0.202| | 80| 311006| 81051| 0.207| | 85| 322111| 90922| 0.220| | 90| 340943| 110478| 0.245| | 95| 377469| 340152| 0.474| | 100| 1479090| 2361373| 0.615|
But I am not really sure how to interpret this information. The way this makes sense to me is that if I use, for instance, tranche 85 as my final SNP subset, I would accept that each novel SNP has 22% chance of being a false positive. However, this corresponds to 90922 SNPs and 1% of the total SNP set, which I am willing to live with and move on with the analysis.
I would like to know if this interpretation correct and if you have any suggestions (i.e. would it make a big difference to choose tranche 90 instead of 85?).