Article
Evaluating the influence of quality control decisions and software algorithms on SNP calling for the affymetrix 6.0 SNP array platform.
Human heredity - 1 Jan 2011
de Andrade Mariza, Atkinson Elizabeth J, Bamlet William R, Matsumoto Martha E, Maharjan Sooraj, Slager Susan L, Vachon Celine M, Cunningham Julie M, Kardia Sharon L R
Abstract excerpt
OBJECTIVE: Our goal was to evaluate the influence of quality control (QC) decisions using two genotype calling algorithms, CRLMM and Birdseed, designed for the Affymetrix SNP Array 6.0. METHODS: Various QC options were tried using the two algorithms and comparisons were made on subject and call rate and on association results using two data sets. RESULTS: For Birdseed, we recommend using the contrast QC instead...
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