SNPInt-GPU：具有多种方法和 GPU 加速的连锁不平衡检测工具。

SNPInt-GPU: Tool for Epistasis Testing with Multiple Methods and GPU Acceleration.

机构信息

Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.

出版信息

Methods Mol Biol. 2021;2212:17-35. doi: 10.1007/978-1-0716-0947-7_2.

Abstract

We present SNPInt-GPU, a software providing several methods for statistical epistasis testing. SNPInt-GPU supports GPU acceleration using the Nvidia CUDA framework, but can also be used without GPU hardware. The software implements logistic regression (as in PLINK epistasis testing), BOOST, log-linear regression, mutual information (MI), and information gain (IG) for pairwise testing as well as mutual information and information gain for third-order tests. Optionally, r scores for testing for linkage disequilibrium (LD) can be calculated on-the-fly. SNPInt-GPU is publicly available at GitHub. The software requires a Linux-based operating system and CUDA libraries. This chapter describes detailed installation and usage instructions as well as examples for basic preliminary quality control and analysis of results.

摘要

我们介绍 SNPInt-GPU，这是一款提供多种统计上位性检验方法的软件。SNPInt-GPU 支持使用 Nvidia CUDA 框架进行 GPU 加速，但也可以在没有 GPU 硬件的情况下使用。该软件实现了逻辑回归（如 PLINK 上位性检验）、BOOST、对数线性回归、互信息（MI）和信息增益（IG）用于成对检验，以及互信息和信息增益用于三阶检验。可选地，可以实时计算用于检测连锁不平衡（LD）的 r 分数。SNPInt-GPU 可在 GitHub 上获得。该软件需要基于 Linux 的操作系统和 CUDA 库。本章详细介绍了安装和使用说明，以及基本初步质量控制和结果分析的示例。