Journal article
A population model for genotyping indels from next-generation sequence data
H Shao, E Bellos, H Yin, X Liu, J Zou, Y Li, J Wang, LJM Coin
Nucleic Acids Research | OXFORD UNIV PRESS | Published : 2013
DOI: 10.1093/nar/gks1143
Open access
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. © 2012 The Author(s) 2012. Published by Oxford University Press.
Grants
Awarded by UK Research and Innovation
Funding Acknowledgements
Major State Basic Research Development Program of China-973 Program [2011CB809201, 2011CB809202, 2011CB809203]; Major Program of National Natural Science Foundation of China [30890032]; Shenzhen Key Laboratory of Transomics Biotechnologies [CXB201108250096A]; the BBSRC research grant [award number BB/H024808/1 to L.J.M.C. and E. B.]. Funding for open access charge: Imperial College open access fund.