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<span style="color: red">'''(Updated: January 2015; latest documentation can always be found at: [http://zhanxw.github.io/rvtests/ http://zhanxw.github.io/rvtests/])'''</span>

 

'''Table of Contents'''

 

** [[#genotype-file-vcf|Genotype file (VCF)]]<br />

** [[#phenotype-file|Phenotype file]]<br />

** [[#covariate-file|Covariate file]]<br />

** [[#trait-transformation|Trait transformation]]<br />

** [[#single-variant-tests|Single variant tests]]<br />

** [[#burden-tests|Burden tests]]<br />

** [[#variable-threshold-models|Variable threshold models]]<br />

** [[#specify-groups-eg-burden-unit|Specify groups (e.g burden unit)]]<br />

* [[#sex-chromosome-analysis|Sex chromosome analysis]]<br />

* [[#kinship-generation|Kinship generation]]<br />

* [[#frequently-asked-questions-faq|Frequently Asked Questions (FAQ)]]<br />

 

 

 

 

= Introduction =

= Introduction =

Rvtests, which stands for Rare Variant tests, is a flexible software package for genetic association studies. It is designed to support unrealted 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 [http://www.1000genomes.com/ 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 studies. It is designed to support unrealted 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 [http://www.1000genomes.com/ 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 is a collaborative effort by Youna Hu, Bingshan Li, Dajiang Liu.

Rvtests is a collaborative effort by Youna Hu, Bingshan Li, Dajiang Liu.