Analysing Quality Measures of Phasing Algorithms in Genome-Wide Haplotyping

  • Sergio Torres-Sánchez
  • Manuel García-Sánchez
  • Nuria Medina-Medina
  • María Mar Abad-Grau
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 222)

Abstract

Inferring haplotype phase is a subject of interest, and given the increasing number of GWAS and related applications, like genetic profiling, it is necessary for phasing algorithms to provide a good performance even when processing large DNA fragments. Most of studies focus on genomic regions of limited length, therefore, we propose to test the most common statistics with genetic regions of variable length. We have found that one of the most used, the switch error, is insufficient when considering long distances: it converges to a constant value which does not truly shows the quality of the inferred phase. Furthermore, the IGP (incorrect genotype percentage) is a much more precise measure of the quality of the algorithm. New phasing algorithms should not care only about the number of switches, because in some cases (classifiers to assess genetic risks, for example) is important to distinguish the haplotype of each parent to obtain better results.

Keywords

haplotype phasing algorithms switch errors genetic maps 

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Copyright information

© Springer International Publishing Switzerland 2013

Authors and Affiliations

  • Sergio Torres-Sánchez
    • 1
  • Manuel García-Sánchez
    • 1
  • Nuria Medina-Medina
    • 1
  • María Mar Abad-Grau
    • 1
  1. 1.Department of Computer Languages and Systems - CITICUniversity of GranadaGranadaSpain

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