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raphael-group / decifer

DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF).
BSD 3-Clause "New" or "Revised" License
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merging development from personal fork #8

Closed brian-arnold closed 3 years ago

brian-arnold commented 3 years ago

Quite a few changes here, all of which have been tested.

  1. We now compute and report the CIs for each cluster, for each sample.
  2. A script to quickly generate decifer input with a VCF file containing SNVs and a CNA file (output from HATCHet)
  3. This script above also outputs a file containing all the unique CN states for a patient, in a format that may be given directly to the generatestatetrees function. This will help respond to the warning regarding skipping mutations because the observed states are not in the state tree file.
  4. Documentation has been made for all these changes.