Details

Autor(en) / Beteiligte

• Serang, Oliver
• Mollinari, Marcelo
• Garcia, Antonio Augusto Franco
• Rapallo, Fabio

Titel

Efficient exact maximum a posteriori computation for bayesian SNP genotyping in polyploids

Ist Teil von

• PloS one, 2012-02, Vol.7 (2), p.e30906-e30906

Ort / Verlag

United States: Public Library of Science

Erscheinungsjahr

2012

Link zum Volltext

Quelle

Free E-Journal (出版社公開部分のみ）

Beschreibungen/Notizen

• The problem of genotyping polyploids is extremely important for the creation of genetic maps and assembly of complex plant genomes. Despite its significance, polyploid genotyping still remains largely unsolved and suffers from a lack of statistical formality. In this paper a graphical bayesian model for SNP genotyping data is introduced. This model can infer genotypes even when the ploidy of the population is unknown. We also introduce an algorithm for finding the exact maximum a posteriori genotype configuration with this model. This algorithm is implemented in a freely available web-based software package SuperMASSA. We demonstrate the utility, efficiency, and flexibility of the model and algorithm by applying them to two different platforms, each of which is applied to a polyploid data set: Illumina GoldenGate data from potato and Sequenom MassARRAY data from sugarcane. Our method achieves state-of-the-art performance on both data sets and can be trivially adapted to use models that utilize prior information about any platform or species.