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eveilyeverafter / HMMancestry

R package using the Forward-Backward algorithm to infer genotypes, recombination hotspots, and gene conversion tracts from low-coverage next-generation sequence data.
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Realistic recombination #2

Closed eveilyeverafter closed 9 years ago

eveilyeverafter commented 9 years ago

In the current simulation functions, recombination only occurs between the same two non-sister chromotids. A more realistic version would allow for recombination to occur between sister chromotids too plus allow for more than one pair of chromotids to recombine per meiosis event. Indeed, empirical data shows that a signature of recombination that sometimes affects all the spores of a tetrad for a given chromosome.

eveilyeverafter commented 9 years ago

The new recombine function in simulate.R now has recombination between any two chromotids.