Abstract
Abstract Copy number variation is one of the common types of structure variation in the human genome. There have been many technologies developed to detect copy number variations and one of them is the SNP array. With the progression of chip technology, we can quickly obtain genome-wide information. A number of algorithms proposed to efficiently extract chromosome copy number variation information from the huge SNP data. The goal of this study is to know how these CNV detection algorithms perform. In this article, we compare four algorithms on HapMap 270 samples from Affymetrix SNP 6.0 array data. The performance is evaluated based on the consistency of the trios and the concordance rate with two published data. According to our analysis, there is not a single CNV detection algorithm outperforming all the other CNV calling methods.