search

PoonLab / OpenRDP

An open-source re-implementation of the RDP4 recombination detection program
GNU General Public License v3.0
45 stars 9 forks source link

Incorporate CHIMAERA method #14

Closed kwade4 closed 3 years ago

kwade4 commented 3 years ago

CHIMAERA is very similar to MaxChi, with only a few modifications. In each triplet, 2 sequences are considered as "parental" and 1 sequence is considered "recombinant".

  1. Monomorphic sites and sites at which neither of the 2 "parental" sequences match the selected "recombinant" are discarded.
  2. Each of the three sequences is encoded as a bit-string where 0 represents a match to one of the "parental" sequences and 0 represents a match to the other "parental" sequence.
  3. Calculate a 2x2 chi squared value in each half of the sliding window.
kwade4 commented 3 years ago

Implemented in commit b92012d