Genome-wide SNP genotyping was performed using the Illumina Human 660 W-Quad_v1_A, (Illumina, San Diego, CA) (n=560,768 SNPs). According to the data set release as well as the quality control and quality assurance policies of the GENEVA consortium(36 (link)), genotypes were not reported for any SNP which had a call rate less than 85% or which had more than 1 replicate error as defined with the HapMap control samples. Identical-by-descent (IBD) coefficients were estimated using 107,014 au-tosomal SNPs with missing call rate < 5% and no closer than 15 kb apart(36 (link)).
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Genome-wide SNP Genotyping and Quality Control
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Variable analysis
independent variables
- None explicitly mentioned
- Genome-wide SNP genotyping data
- SNPs with call rate less than 85%
- SNPs with more than 1 replicate error as defined with the HapMap control samples
- Autosomal SNPs with missing call rate < 5% and no closer than 15 kb apart
- HapMap control samples used to define replicate errors
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