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PedKin : compute kinship coefficients

B. Kirkpatrick, S. Ge, and L. Wang. Efficient computation of the kinship coefficients. Bioinformatics, bty725. 2018.


The Problem

Given a pedigree of individuals, founder kinship coefficients, and individuals of interest, compute the kinship and inbreeding coefficients for all the individuals of interest in the pedigree.

These coefficients indicate the genetic similarity between pairs of individuals in the genealogy.

This is the fastest known algorithm for computing the kinship coefficients. We either compute exact coefficients or estimate the coefficients.

This is the only algorithm that considers the inbreeding coefficients of the founders.


Build and Run

Build

> g++ -O3 -o pedkin pedigree-kinship.cpp

USAGE: ./pedkin [algorithm] (iterations) [ped file] [founder kinship] [indiv interest] [kinship output]


What is the license?

GNU GPL v2.0

The PDF document describing the algorithm is to be distributed both with the source code and with any compiled binaries.

Academic users are to cite: B. Kirkpatrick, S. Ge, and L. Wang. Efficient computation of the kinship coefficients. Bioinformatics, bty725, https://doi.org/10.1093/bioinformatics/bty725. 2018.


Download

PedKin



Contact

bbkirk@intrepidnetcomputing.com







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