HapMonster: A statistically unified approach for variant calling and haplotyping based on phase-informative reads

Kaname Kojima, Naoki Nariai, Takahiro Mimori, Yumi Yamaguchi-Kabata, Yukuto Sato, Yosuke Kawai, Masao Nagasaki

研究成果: Conference contribution

6 被引用数 (Scopus)

抄録

Haplotype phasing is essential for identifying disease-causing variants with phase-dependent interactions as well as for the coalescent-based inference of demographic history. One of approaches for estimating haplotypes is to use phase-informative reads, which span multiple heterozygous variant positions. Although the quality of estimated variants is crucial in haplotype phasing, accurate variant calling is still challenging due to errors on sequencing and read mapping. Since some of such errors can be corrected by considering haplotype phasing, simultaneous estimation of variants and haplotypes is important. Thus, we propose a statistically unified approach for variant calling and haplotype phasing named HapMonster, where haplotype phasing information is used for improving the accuracy of variant calling and the improved variant calls are used for more accurate haplotype phasing. From the comparison with other existing methods on simulation and real sequencing data, we confirm the effectiveness of HapMonster in both variant calling and haplotype phasing.

本文言語English
ホスト出版物のタイトルAlgorithms for Computational Biology - First International Conference, AlCoB 2014, Proceedings
出版社Springer-Verlag
ページ107-118
ページ数12
ISBN(印刷版)9783319079523
DOI
出版ステータスPublished - 2014 1 1
イベント1st International Conference on Algorithms for Computational Biology, AlCoB 2014 - Tarragona, Spain
継続期間: 2014 7 12014 7 3

出版物シリーズ

名前Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
8542 LNBI
ISSN(印刷版)0302-9743
ISSN(電子版)1611-3349

Other

Other1st International Conference on Algorithms for Computational Biology, AlCoB 2014
CountrySpain
CityTarragona
Period14/7/114/7/3

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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