Humanomni2.5 8 platform

Human genotyping array data is from Illumina HumanOmni2.5-8 platform. This array has about 2.37 million tag SNPs from 1000 genomes pilot project with MAF ≥2.5%. Illumina Inc. supplied genotypes for all the samples from HumanOmni2.5-8 by performing Illumina Infinium LCG assay and thereupon calling the genotypes using their propriety software called GenomeStudio. They provide genotype for each of these probes with GenCall scores. Illumina recommends a GenCall score cut-off of 0.15 for their infinium assay based products
[20 (link)]. This recommended GenCall score cut-off of 0.15 was used to test the concordance with the GATK and CASAVA pipelines.

Genotyping was performed using Illumina Human Omni2.5-8 platform. The HumanOmni2.5-8 BeadChip delivers comprehensive coverage of both common and rare SNP content from the 1000 Genomes Project (1kGP; MAF > 2.5 %), designed to be maximally informative for diverse world populations. It is able to identify 2,379,855 polymorphisms. The scan protocol followed the standard Illumina procedures using Illumina BeadXpress Reader. The microarray data was analyzed with GenomeStudio V2011.1 and GT module 1.9.4 using default analysis settings. Each SNP is analyzed independently to cluster and identify genotypes. Genotype calls are generated by comparing experimental data with those in the supplied cluster file(*.egt). Calls are generally highly accurate and unambiguous for high quality samples.