Analysis of concordance of different haplotype block partitioning algorithms

Background: Different classes of haplotype block algorithms exist and the ideal dataset to assess their performance would be to comprehensively re-sequence a large genomic region in a large population. Such data sets are expensive to collect. Alternatively, we performed coalescent simulations to generate haplotypes with a high marker density and compared block partitioning results from diversity based, LD based, and information theoretic algorithms under different values of SNP density and allele frequency. Results: We simulated 1000 haplotypes using the standard coalescent for three world populations

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Amit R. Indap, Gabor T. Marth, Craig A. Struble, Peter J. Tonellato, Michael Olivier
• Keywords: Algorithms, Allele Frequency, BMCBI 2005, Haplotypes