Likelihood-based complex trait association testing for arbitrary depth sequencing data.

ABSTRACT:

Unlabelled

In next generation sequencing (NGS)-based genetic studies, researchers typically perform genotype calling first and then apply standard genotype-based methods for association testing. However, such a two-step approach ignores genotype calling uncertainty in the association testing step and may incur power loss and/or inflated type-I error. In the recent literature, a few robust and efficient likelihood based methods including both likelihood ratio test (LRT) and score test have been proposed to carry out association testing without intermediate genotype calling. These methods take genotype calling uncertainty into account by directly incorporating genotype likelihood function (GLF) of NGS data into association analysis. However, existing LRT methods are computationally d

SUBMITTER: Yan S 

PROVIDER: S-EPMC4668777 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature