Estimation of allele frequency and association mapping using next-generation sequencing data

Su Yeon Kim, Kirk E Lohmueller, Anders Albrechtsen, Yingrui Li, Thorfinn Sand Korneliussen, Geng Tian, Niels Grarup, Tao Jiang, Gitte Andersen, Daniel Witte, Torben Jorgensen, Torben Hansen, Oluf Pedersen, Jun Wang, Rasmus Nielsen

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Abstract

Estimation of allele frequency is of fundamental importance in population genetic analyses and in association mapping. In most studies using next-generation sequencing, a cost effective approach is to use medium or low-coverage data (e.g., <15X). However, SNP calling and allele frequency estimation in such studies is associated with substantial statistical uncertainty because of varying coverage and high error rates.
Original languageEnglish
JournalB M C Bioinformatics
Volume12
Pages (from-to)231
Number of pages16
ISSN1471-2105
DOIs
Publication statusPublished - 2011

Keywords

  • Gene Frequency
  • Genetics, Population
  • Genotype
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Likelihood Functions
  • Polymorphism, Single Nucleotide
  • Sequence Analysis, DNA

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