Multiple mutations in same gene in one tree

[KristianaKGrigoriadis]

Hi,

Thank you for the clear instructions on installing and running RECAP.

I have noticed that when I include patients that have a driver mutation in a gene that appears either:

• in more than one mutation cluster (e.g. gene MGA in the following example):
  1 #trees for PATIENT1
  4 #edges
  GL TP53;MGA
  KMT2B SEPT12;MGA;PASK;CDH1;CDKN2C
  TP53;MGA ARHGAP35
  TP53;MGA KMT2B

• more than once within one mutation cluster (e.g. gene CTNNB1 in the following example):
  1 #trees for PATIENT2
  2 #edges
  GL PIK3CA;EGFR
  PIK3CA;EGFR CTNNB1;CTNNB1

RECAP does not run, and the following error is returned:

terminate called after throwing an instance of 'std::runtime_error'
  what():  Error: completing patient trees with missing mutations
Aborted

Is this a known feature of the tool, and would the RECAP input data have to be preprocessed to deal with such cases (e.g. selecting only one mutation cluster within a tree to harbour the gene mutation)? I would assume that it could be biologically plausible that more than one cluster could have a mutation in the same gene, for example in the instance of parallel evolution. How would the authors suggest dealing with such cases?

Thank you very much.