It detects IBD accurately and rapidly using an embedded likelihood ratio test.
Parente2: A fast and accurate method for detecting identity by descent.
Jesse M. Rodriguez*, Sivan Bercovici*, Lin Huang, Roy Frostig, Serafim Batzoglou.
Genome Research. Published in Advance October 1, 2014, doi:10.1101/gr.173641.114
An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embeddeded Likelihood-Ratio Test.
Jesse M. Rodriguez, Serafim Batzoglou, Sivan Bercovici.
Presented at RECOMB 2013 in Beijing, China.
Parente and Parente2 are based on a likelihood ratio, comparing the likelihood of the data based on a model that assumes no IBD is present versus the likelihood of the data based on a model that assumes IBD is present.
In the non-IBD model, genotypes are assumed to be generated from four distinct haplotypes, allowing for some genotyping errors:
In the IBD model, genotypes are assumed to be generated from only three distinct haplotypes, allowing for some genotyping errors: