Rapid genotype refinement for whole-genome sequencing data using multi-variate normal distributions.
Bioinformatics
; 32(15): 2306-12, 2016 08 01.
Article
em En
| MEDLINE
| ID: mdl-27153730
ABSTRACT
MOTIVATION 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. RESULTS:
Our method 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- and high-coverage samples. AVAILABILITY AND IMPLEMENTATION The source code is available at https//github.com/illumina/marvin CONTACT rarthur@illumina.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Base de dados:
MEDLINE
Assunto principal:
Software
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Desequilíbrio de Ligação
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Genótipo
Limite:
Humans
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2016
Tipo de documento:
Article
País de afiliação:
Reino Unido