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fpbarthel / GLASS

GLASS consortium
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Williams et al Neutralitytestr #107

Closed fpbarthel closed 5 years ago

fpbarthel commented 5 years ago

See the R package https://github.com/marcjwilliams1/neutralitytestr, following discussions with Javad:

  1. plot vafs from primary and recurrence against each other
  2. Filter out mutations that are non-diploid (use CNV filter) (edited)
  3. Implement at 25X threshold for local read depth (ref_count + alt_count), which should have a 10% error in VAF per the calculation on page 2 of Javad’s paper
  4. Javad said that it would NOT be ideal to use the VAFs of all tumors in a group UNLESS you were to assume they all had the same mutation rate (they do not)
Kcjohnson commented 5 years ago

Closing this issue as we largely solved this issue by applying neutralitytestR on the cohort-level data.