Assessing consistency between versions of genotype-calling algorithm birdseed for the genome-wide human SNP array 6.0 using HapMap samples

Abstract

Highly accurate and reproducible genotype calling is a key to success of genome-wide association studies (GWAS) since errors introduced by calling algorithms can lead to inflation of false associations between genotype and phenotype. The Affymetrix Genome-Wide Human SNP Array 6.0 is widely utilized and was used in the current GWAS. Birdseed, a genotype-calling algorithm for this chip, is available in two versions. It is important to know the reproducibility between the two versions. We assessed the inconsistency in genotypes called by the two versions of Birdseed and examined the propagation of the genotype inconsistency to the downstream association analysis by using the 270 HapMap samples. Our results revealed that genotypes called from version-1 and version-2 of Birdseed were slightly different and the inconsistency in genotypes propagated to the downstream association analysis. © 2010 Springer Science+Business Media, LLC.