MOSAIC

MOSAIC is a tool for modelling multiway admixture using dense genotype data.
See preprint for details.

Given a set of potentially admixed haplotypes (targets) and multiple labelled sets of potentially related haplotypes (panels),
MOSAIC will infer the most recent admixture events occurring in the targets in terms of the panels.

It is not necessary that any of the panels are a good surrogate for the unseen mixing groups as MOSAIC will infer parameters controlling:
1. The stochastic relationship between panels and ancestral groups.
2. Timings and ancestry proportions of the admixture events.
3. Recombination rates before and after admixture.
4. Mutation / error rates for the haplotypes.

Phasing improvements in light of the admixture model are performed and local ancestry along the genome is estimated.

Code

Click to download an R Package version 1.2 including README.txt and example data, demos, etc.

Human Genome Diversity Panel

A browser of MOSAIC results on an extended version of the Human Genome Diversity Panel demonstrates the flexibility of the model.
Click on the map below to open an interactive Google Maps interface to the results.

(Also available as a simple text list.)