ISHAPE: new rapid and accurate software for haplotyping

Background: We have developed a new haplotyping program based on the combination of an iterative multiallelic EM algorithm (IEM), bootstrap resampling and a pseudo Gibbs sampler. The use of the IEM-bootstrap procedure considerably reduces the space of possible haplotype configurations to be explored, greatly reducing computation time, while the adaptation of the Gibbs sampler with a recombination model on this restricted space maintains high accuracy. On large SNP datasets (>30 SNPs), we used a segmented approach based on a specific partition-ligation strategy. We compared this software, Ishape (Iterative Segmented HAPlotyping by Em), with reference programs such as Phase, Fastphase, and PL-EM. Analogously with Phase, there are 2 versions of Ishape: Ishape1 which uses a simple coalescence model for the pseudo Gibbs sampler step, and Ishape2 which uses a recombination model instead. Results: We tested the program on 2 types of real SNP datasets derived from Hapmap: adjacent SNPs (hi...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Olivier Delaneau, Cédric Coulonges, Pierre-Yves Boëlle, George Nelson, Jean-Louis Spadoni, Jean-François Zagury
• Keywords: Adjacent Snps, BMCBI 2007, Pseudo Gibbs, SNPs