Maximal Perfect Haplotype Blocks with Wildcards
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Updated: Dec 20, 2025

Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
Lucia Williams1, Brendan Mumey1
1Gianforte School of Computing, Montana State University, Bozeman, MT 59717, USA.
Abstract:
Recent work provides the first method to measure the relative fitness of genomic variants within a population that scales to large numbers of genomes. A key component of the computation involves finding maximal perfect haplotype blocks from a set of genomic samples for which SNPs (single-nucleotide polymorphisms) have been called. Often, owing to low read coverage and imperfect assemblies, some of the SNP calls can be missing from some of the samples. In this work, we consider the problem of finding maximal perfect haplotype blocks where some missing values may be present. Missing values are treated as wildcards, and the definition of maximal perfect haplotype blocks is extended in a natural way. We provide an output-linear time algorithm to identify all such blocks and demonstrate the algorithm on a large population SNP dataset. Our software is publicly available.
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