4.6 years ago by
Washington University in St. Louis, MO
That actually sounds about right, depending on the parameters that you used. Some notes:
1) I'd expect the concordance to be fairly high for high-VAF variants, but when you get down to rare subclonal, variants, where only a small amount of read support exists, callers can handle those cases very differently.
2) Do you want high specificity or sensitivity - each caller has made it's own set of tradeoffs between the two, and figuring out the 'sweet spot' for you will depend on your experiment.
3) Intersecting the data will generally improve specificity (I'd expect 90%+ if something is called by all three callers), but will lose you a lot of the true positives at low VAF that may only be picked up by one of the statistical models. Again, just depends on what you're hoping to accomplish with your experiment.