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Protocols

RVTESTS specifications

Information


Unique identifier OMICS_11296
Name RVTESTS
Alternative name Rare Variant TESTS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data It takes VCF format as genotype input file and takes PLINK format phenotype file and covariate file.
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Xiaowei Zhan

Publication for Rare Variant TESTS

RVTESTS citations

 (55)
library_books

WISARD: workbench for integrated superfast association studies for related datasets

2018
BMC Med Genomics
PMCID: 5918457
PMID: 29697360
DOI: 10.1186/s12920-018-0345-y

[…] ability and computational efficiency of WISARD, we consider the recently developed toolsets for large-scale genetic dataset analyses with family-based samples: GEMMA for variant-level analyses [] and Rvtests for gene-level tests []. Rvtests was the most recently developed toolset and provides most comprehensive features for rare variant association analyses. famSKAT [] is also considered for famil […]

library_books

Identification of rare sequence variation underlying heritable pulmonary arterial hypertension

2018
Nat Commun
PMCID: 5897357
PMID: 29650961
DOI: 10.1038/s41467-018-03672-4

[…] s by combining variance-component and burden tests. Variants were filtered based on MAF as specified above, and only PTV and missense variants were included. For the analysis we implemented SKAT-O in RvTests v1.9.9 with default parameters and weights being Beta(1,25), and applying a correction for read length, gender and the first five principal components of the ethnicity PCA. Variants were colla […]

library_books

Another Round of “Clue” to Uncover the Mystery of Complex Traits

2018
Genes
PMCID: 5852557
PMID: 29370075
DOI: 10.3390/genes9020061

[…] pe of interest is the most popular method. Many analysis tools have been developed for these analyses such as BioBin [], Sequence Kernel Association Test (SKAT) [] , Variant Association Tools [], and RVTESTS []. Several genes containing rare variants have been identified with moderate to high effects on complex traits such as the association of low-frequency variants in IFIH1 with type 2 diabetes […]

library_books

Exome wide rare variant analyses of two bone mineral density phenotypes: the challenges of analyzing rare genetic variation

2018
Sci Rep
PMCID: 5760616
PMID: 29317680
DOI: 10.1038/s41598-017-18385-9

[…] variants can often be accurately estimated when the genotyped variants are used as a skeleton framework for imputation against a large panel of individuals who have been sequenced.Most currently used rare-variant tests analyze one phenotype—that is, they focus on the association between a set of rare variants and a single phenotype. However, multiple correlated phenotypes are often collected. Ther […]

library_books

Exome chip meta analysis identifies novel loci and East Asian specific coding variants contributing to lipid levels and coronary artery disease

2017
Nat Genet
PMCID: 5899829
PMID: 29083407
DOI: 10.1038/ng.3978

[…] cases and controls were analyzed separately.We performed both single variant and gene-level association tests. Single variant analyses in each cohort were carried out using either RAREMETALWORKER or RVTESTS, both of which generate single variant score statistics and their covariance matrix between single marker statistics. The test statistics, as visualized in a quantile–quantile plot, appeared w […]

call_split

Exome wide association study of plasma lipids in >300,000 individuals

2017
Nat Genet
PMCID: 5709146
PMID: 29083408
DOI: 10.1038/ng.3977
call_split See protocol

[…] we collected single variant score statistics and their covariance matrix for variants in sliding windows across the genome. Summary association test statistics were generated using RAREMETALWORKER or RVTESTS. Using summary association statistics collected from each study, we performed meta-analysis of single variant association tests using the Mantel-Haenszel test and constructed burden, SKAT and […]

Citations

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RVTESTS institution(s)
Department of Clinical Science, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA; Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA; A9Com Inc, Palo Alto, CA, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA; Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA; Division of Biostatistics and Bioinformatics, Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA; Institute for Personalized Medicine, Penn State College of Medicine, Hershey, PA, USA
RVTESTS funding source(s)
This work was supported by National Institutes of Health grants 1R01HG008983-01, 1R21DA040177-01, 1R01DA037904-01A1, R01HG006857 and R01HG007022.

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