GeneSeq – LD-based SNP genotype calling from shotgun sequencing reads


The 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 exploting 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.

GeneSeq source code

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This material is based upon work supported in part by the National Science Foundation under Grants No. IIS-0546457, IIS-0916948, and DBI-0543365. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.