XPAT: a toolkit to conduct cross-platform association studies with heterogeneous sequencing datasets.

ABSTRACT: High-throughput sequencing data are increasingly being made available to the research community for secondary analyses, providing new opportunities for large-scale association studies. However, heterogeneity in target capture and sequencing technologies often introduce strong technological stratification biases that overwhelm subtle signals of association in studies of complex traits. Here, we introduce the Cross-Platform Association Toolkit, XPAT, which provides a suite of tools designed to support and conduct large-scale association studies with heterogeneous sequencing datasets. XPAT includes tools to support cross-platform aware variant calling, quality control filtering, gene-based association testing and rare variant effect size estimation. To evaluate the performance of XPAT, we con

SUBMITTER: Yu Y 

PROVIDER: S-EPMC5888834 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature