RT Journal Article
SR Electronic
T1 Rapid Genotype Refinement for Whole-Genome Sequencing Data using Multi-Variate Normal Distributions
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 031484
DO 10.1101/031484
A1 Rudy Arthur
A1 Jared O’Connell
A1 Ole Schulz-Trieglaff
A1 Anthony J. Cox
YR 2015
UL http://biorxiv.org/content/early/2015/11/12/031484.abstract
AB Whole-genome low-coverage sequencing has been combined with linkage-disequilibrium (LD) based genotype refinement to accurately and cost-effectively infer genotypes in large cohorts of individuals. Most genotype refinement methods are based on hidden Markov models, which are accurate but computationally expensive. We introduce an algorithm that models LD using a simple multivariate Gaussian distribution. The key feature of our algorithm is its speed, it is hundreds of times faster than other methods on the same data set and its scaling behaviour is linear in the number of samples. We demonstrate the performance of the method on both low-coverage and high-coverage samples.Availability: The source code is available at https://github.com/sequencing/marvinContact: rarthur{at}illumina.com