Genotype calling from next-generation sequencing data using haplotype information of reads.

doi:10.1093/bioinformatics/bts047

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Article

Genotype calling from next-generation sequencing data using haplotype information of reads.

Bioinformatics (Oxford, England) - 1 Apr 2012

Zhi Degui, Wu Jihua, Liu Nianjun, Zhang Kui

Abstract excerpt

MOTIVATION: Low coverage sequencing provides an economic strategy for whole genome sequencing. When sequencing a set of individuals, genotype calling can be challenging due to low sequencing coverage. Linkage disequilibrium (LD) based refinement of genotyping calling is essential to improve the accuracy. Current LD-based methods use read counts or genotype likelihoods at individual potential polymorphic sites...

Topics

Algorithms
Computational Biology
Computer Simulation
Genome-Wide Association Study
Genotype
HapMap Project
Haplotypes
Humans
Linkage Disequilibrium
Markov Chains
Models, Statistical
Sequence Analysis, DNA
Software

Source

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Identifiers

PMID: 22285565
DOI: 10.1093/bioinformatics/bts047
PMCID: PMC3493122

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