CANOES: detecting rare copy number variants from whole exome sequencing data.

ABSTRACT: We present CANOES, an algorithm for the detection of rare copy number variants from exome sequencing data. CANOES models read counts using a negative binomial distribution and estimates variance of the read counts using a regression-based approach based on selected reference samples in a given dataset. We test CANOES on a family-based exome sequencing dataset, and show that its sensitivity and specificity is comparable to that of XHMM. Moreover, the method is complementary to Gaussian approximation-based methods (e.g. XHMM or CoNIFER). When CANOES is used in combination with these methods, it will be possible to produce high accuracy calls, as demonstrated by a much reduced and more realistic de novo rate in results from trio data.

SUBMITTER: Backenroth D 

PROVIDER: S-EPMC4081054 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature