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Bioinformatics. 2012 Mar 15;28(6):838-44. doi: 10.1093/bioinformatics/bts033. Epub 2012 Jan 17.

Exact coalescent simulation of new haplotype data from existing reference haplotypes.

Author information

1
Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA. chulkang@usc.edu

Abstract

MOTIVATION:

We introduce a coalescent-based method (RECOAL) for the simulation of new haplotype data from a reference population of haplotypes. A coalescent genealogy for the reference haplotype data is sampled from the appropriate posterior probability distribution, then a coalescent genealogy is simulated which extends the sampled genealogy to include new haplotype data. The new haplotype data will, therefore, contain both some of the existing polymorphic sites and new polymorphisms added based on the structure of the simulated coalescent genealogy. This allows exact coalescent simulation of new haplotype data, compared with other methods which are more approximate in nature.

RESULTS:

We demonstrate the performance of our method using a variety of data simulated under a coalescent model, before applying it to data from the 1000 Genomes project.

PMID:
22257666
PMCID:
PMC3307111
DOI:
10.1093/bioinformatics/bts033
[Indexed for MEDLINE]
Free PMC Article

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