2SNP: scalable phasing based on 2-SNP haplotypes

被引：26

作者：

Brinza, D ^{[1
]}

Zelikovsky, A ^{[1
]}

机构：

[1] Georgia State Univ, Dept Comp Sci, Atlanta, GA 30303 USA

来源：

BIOINFORMATICS | 2006年 / 22卷 / 03期

关键词：

D O I：

10.1093/bioinformatics/bti785

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

2SNP software package implements a new very fast scalable algorithm for haplotype inference based on genotype statistics collected only for pairs of SNPs. This software can be used for comparatively accurate phasing of large number of long genome sequences, e.g. obtained from DNA arrays. As an input 2SNP takes genotype matrix and outputs the corresponding haplotype matrix. On datasets across 79 regions from HapMap 2SNP is several orders of magnitude faster than GERBIL and PHASE while matching them in quality measured by the number of correctly phased genotypes, single-site and switching errors. For example, 2SNP requires 41 s on Pentium 4 2 Ghz processor to phase 30 genotypes with 1381 SNPs (ENm010.7p15:2 data from HapMap) versus GERBIL and PHASE requiring more than a week and admitting no less errors than 2SNP.

引用

页码：371 / 373

页数：3

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