A new model calling procedure for Illumina BeadArray data.

ABSTRACT:

Background

Accurate genotype calling for high throughput Illumina data is an important step to extract more genetic information for a large scale genome wide association studies. Many popular calling algorithms use mixture models to infer genotypes of a large number of single nucleotide polymorphisms in a fast and efficient way. In practice, mixture models are mostly restricted to infer genotypes for common SNPs where their minor allele frequencies are quite large. However, it is still challenging to accurately genotype rare variants, especially for some rare variants where the boundaries of their genotypes are not clearly defined.

Results

To further improve the call accuracy and the quality of genotypes on rare variants, a new model calling procedure, named M-D, is proposed

SUBMITTER: Li G 

PROVIDER: S-EPMC4921002 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature