SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data.

ABSTRACT:

Background

High throughput microarray-based single nucleotide polymorphism (SNP) genotyping has revolutionized the way genome-wide linkage scans and association analyses are performed. One of the key features of the array-based GeneChip Mapping 10K Array from Affymetrix is the automated SNP calling algorithm. The Affymetrix algorithm was trained on a database of ethnically diverse DNA samples to create SNP call zones that are used as static models to make genotype calls for experimental data. We describe here the implementation of clustering algorithms on large training datasets resulting in improved SNP call rates on the 10K GeneChip.

Results

A database of 948 individuals genotyped on the GeneChip Mapping 10K 2.0 Array was used to identify 822 SNPs that were called consiste

SUBMITTER: Huentelman MJ 

PROVIDER: S-EPMC1280925 | biostudies-literature | 2005 Oct

REPOSITORIES: biostudies-literature