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David Altshuler and colleagues describe analysis for integrating genotype calling of SNPs, common copy number polymorphisms and rare CNVs, implemented in a suite of software programs collectively named Birdsuite.
Matt Hurles and colleagues present a general statistical framework for copy number variation (CNV) association tests in a case-control study design. They show that existing strategies for CNV association with binary disease phenotypes are complicated by differential errors and poor clustering quality. Here they report new methods, robust to these factors, which apply likelihood ratio testing to constrained Gaussian mixture models of quantitative CNV signals in cases and controls. Their methods are assay and platform independent, and implemented in freely available CNVtools software.