GeneSeq package provides methods to call SNP genotypes and infer haplotypes for a single individual given reads produced by whole-genome shotgun sequencing using high-throughput technologies such as 454, Illumina, and ABI SOLiD. GeneSeq yields high genotype calling accuracy even from low read coverage by ecploting linkage disequilibrium patterns extracted from a reference panel such as those generated by the international Hapmap project. Genotype and haplotype inference is performed efficiently using a hierarchical factorial hidden Markov model (HF-HMM) integrating allele coverage information extracted from read data with haplotype frequencies inferred from the reference panel.
Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut
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J. Duitama and J. Kennedy and S. Dinakar and Y. Hernandez and Y. Wu and I.I. Mandoiu,
Linkage Disequilibrium Based Genotype Calling from Low-Coverage Shotgun Sequencing Reads,
BMC Bioinformatics 12(Suppl 1):S53, 2011