Parente2 is a method for detecting relatedness.

It detects IBD accurately and rapidly using an embedded likelihood ratio test.

Parente2

Version 0.1 of Parente2 is currently available for 64-bit Linux.

Parente2 can be applied in conjunction with SpeeDB, which significantly reduces the running time and often modestly boosts the accuracy.

Publications

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.

Features

  • Accurate

    High accuracy enables Parente2 to be applied to large datasets.
  • No cohort phasing required

    Once trained, infers IBD directly on genotypes.
  • Fast

    Uses an efficient sliding-window-based model.
  • Parallelizable

    Regions along the chromosome are analyzed independently.

Methods

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:

Contact

Questions or comments may be directed to Jesse Rodriguez at jesserod at cs dot stanford dot edu.