Commit 1ac2159d authored by zhanxw's avatar zhanxw

fix conflicts

parents 0b8f2daf 90ed195b
......@@ -41,11 +41,15 @@
[![Build Status](https://travis-ci.org/zhanxw/rvtests.png?branch=master)](https://travis-ci.org/zhanxw/rvtests)
(Updated: June 2017)
(Updated: Aug 2017)
# Introduction
Rvtests, which stands for Rare Variant tests, is a flexible software package for genetic association studies. It is designed to support unrelated individual or related (family-based) individuals. Both quantitative trait and binary trait are supported. It includes a variety of association tests (e.g. single variant score test, burden test, variable threshold test, SKAT test, fast linear mixed model score test). It takes [VCF][vcf] format as genotype input file and takes PLINK format phenotype file and covariate file. From our practice, it is capable to analyze 8,000 related individuals using less than 400 Mb memory.
Rvtests, which stands for Rare Variant tests, is a flexible software package for genetic association analysis for sequence datasets. Since its inception, rvtests was developed as a comprehensive tool to support genetic association analysis and meta-analysis. It can analyze both unrelated individual and related (family-based) individuals for both quantitative and binary outcomes. It includes a variety of association tests (e.g. single variant score test, burden test, variable threshold test, SKAT test, fast linear mixed model score test). It takes [VCF][vcf] format as genotype input file and takes PLINK format phenotype file and covariate file.
With new implementation of the BOLT-LMM/MINQUE algorithm as well as a series of software engineering optimizations, our software package is capable of analyzing datasets of up to 1,000,000 individuals in linear mixed models on a computer workstation, which makes our tool one of the very few options for analyzing large biobank scale datasets, such as UK Biobank. RVTESTS supports both single variant and gene-level tests. It also allows for highly effcient generation of covariance matrices between score statistics in RAREMETAL format, which can be used to support the next wave of meta-analysis that incorporates large biobank datasets.
A (much) larger sample size can be handled using linear regression or logistic regression models.
[vcf]: http://www.1000genomes.com/
......@@ -59,8 +63,13 @@ Bioinformatics 2016 32: 1423-1426. [doi:10.1093/bioinformatics/btw079](http://bi
# Download
Source files can be downloaded from [github](https://github.com/zhanxw/rvtests/archive/master.zip) or [github page](https://github.com/zhanxw/rvtests).
Executable binary files (for Linux 64bit) can be downloaded from [here](https://github.com/zhanxw/rvtests/releases).
Source files can be downloaded from [github](https://github.com/zhanxw/rvtests/archive/master.zip) or [github page](https://github.com/zhanxw/rvtests). Under Linux, you may simply use
```
git clone https://github.com/zhanxw/rvtests
```
to retrieve the latest distribution for rvtests. To install, go to the rvtests folder and type `make`.
We also provided executable binary files (for Linux 64bit), which can be downloaded from [here](https://github.com/zhanxw/rvtests/releases).
# Quick tutorial
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