Variant association tools for quality control and analysis of large-scale sequence and genotyping array data.

ABSTRACT: Currently there is great interest in detecting associations between complex traits and rare variants. In this report, we describe Variant Association Tools (VAT) and the VAT pipeline, which implements best practices for rare-variant association studies. Highlights of VAT include variant-site and call-level quality control (QC), summary statistics, phenotype- and genotype-based sample selection, variant annotation, selection of variants for association analysis, and a collection of rare-variant association methods for analyzing qualitative and quantitative traits. The association testing framework for VAT is regression based, which readily allows for flexible construction of association models with multiple covariates and weighting themes based on allele frequencies or predicted functionali

SUBMITTER: Wang GT 

PROVIDER: S-EPMC4067555 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature