M(3)-S: a genotype calling method incorporating information from samples with known genotypes.

ABSTRACT:

Background

A key challenge in analyzing high throughput Single Nucleotide Polymorphism (SNP) arrays is the accurate inference of genotypes for SNPs with low minor allele frequencies. A number of calling algorithms have been developed to infer genotypes for common SNPs, but they are limited in their performance in calling rare SNPs. The existing algorithms can be broadly classified into three categories, including: population-based methods, SNP-based methods, and a hybrid of the two approaches. Despite the relatively better performance of the hybrid approach, it is still challenging to analyze rare SNPs.

Results

We propose to utilize information from samples with known genotypes to develop a two stage genotyping procedure, namely M(3)-S, for rare SNP calling. This new approac

SUBMITTER: Li G 

PROVIDER: S-EPMC4669649 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature