M(3): an improved SNP calling algorithm for Illumina BeadArray data.

ABSTRACT:

Summary

Genotype calling from high-throughput platforms such as Illumina and Affymetrix is a critical step in data processing, so that accurate information on genetic variants can be obtained for phenotype-genotype association studies. A number of algorithms have been developed to infer genotypes from data generated through the Illumina BeadStation platform, including GenCall, GenoSNP, Illuminus and CRLMM. Most of these algorithms are built on population-based statistical models to genotype every SNP in turn, such as GenCall with the GenTrain clustering algorithm, and require a large reference population to perform well. These approaches may not work well for rare variants where only a small proportion of the individuals carry the variant. A fundamentally different approach, implem

SUBMITTER: Li G 

PROVIDER: S-EPMC3268244 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature