John St. John

Added some new partially implemented features, along with tests which should not yet be passing.

Woot! Super close. Ok so Frank, the only thing I need to change is the known sites filter. The thing is that this is not a binary keep/throw away kind...

Thanks Frank!! On Sat, Aug 1, 2015 at 6:09 PM, Frank Austin Nothaft < [email protected]> wrote: > @jstjohn https://github.com/jstjohn oh, hah! Goofy mistake on my side. > I think that...

Would it make sense to incorporate ideas from Strelka as well? Specifically ability to do indels? MuTect is the best out there now for mutations though. This would be a...

Is this patent application going to get in our way? I have some experience reimplementing Mutect, but then I found this: https://www.google.com/patents/WO2014036167A1?cl=en&dq=mutect+getz&hl=en&sa=X&ei=YBPLVJfoHsOtogT7zIGgBw&ved=0CB0Q6AEwAA

The statistical model looks nearly complete so far. I am starting to pull @tdanford's mutect code into a fork of your `common-filters` branch @fnothaft. I didn't see a calculation for...

Tests are progressing nicely. Maybe 50% done with testing/fixing the likelihood model. Found a few bugs that were a result of @tdanford getting tricked by Nature's poor equation formatting. When...

Just finished up some initial tests and opened the pr #167 to track progress.

Quick status update on mutect filters that are functions of the alleles/reads supporting the mutation in the tumor (where 90% of the special sauce lies). ### Done/potentially needs testing: -...

marking all complete, although more tests need to be written on everything other than the second, fourth, and final bullet points above. Basically the sum of mismatching bases needs to...