A population model for genotyping indels from next-generation sequence data

Shao, Haojing, Bellos, Evangelos, Yin, Hanjiudai, Liu , Xiao, Zou, Jing, Li, Yingrui, Wang, Jun and Coin, Lachlan J. M. (2013) A population model for genotyping indels from next-generation sequence data. Nucleic Acids Research, 41 3: e46.1-e46.6. doi:10.1093/nar/gks1143

Author Shao, Haojing
Bellos, Evangelos
Yin, Hanjiudai
Liu , Xiao
Zou, Jing
Li, Yingrui
Wang, Jun
Coin, Lachlan J. M.
Title A population model for genotyping indels from next-generation sequence data
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 0305-1048
Publication date 2013-02-01
Year available 2012
Sub-type Article (original research)
DOI 10.1093/nar/gks1143
Open Access Status DOI
Volume 41
Issue 3
Start page e46.1
End page e46.6
Total pages 6
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Subject 1311 Genetics
Abstract Insertion and deletion polymorphisms (indels) are an important source of genomic variation in plant and animal genomes, but accurate genotyping from low-coverage and exome next-generation sequence data remains challenging. We introduce an efficient population clustering algorithm for diploids and polyploids which was tested on a dataset of 2000 exomes. Compared with existing methods, we report a 4-fold reduction in overall indel genotype error rates with a 9-fold reduction in low coverage regions.
Keyword Biochemistry & Molecular Biology
Biochemistry & Molecular Biology
Q-Index Code C1
Q-Index Status Provisional Code
Grant ID 2011CB809201
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
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