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

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.

SUBMITTER: Shao H 

PROVIDER: S-EPMC3562001 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature