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
Acknowledgment and Disclaimer
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.