Rvtests 2.1.0-foss-2021aRvtests, 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/BGEN/PLINK format as genotype input file and takes PLINK format phenotype file and covariate file.
Accessing Rvtests 2.1.0-foss-2021a
To load the module for Rvtests 2.1.0-foss-2021a please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):
module load Rvtests/2.1.0-foss-2021a
BEAR Apps Version
For more information visit the Rvtests website.
This version of Rvtests has a direct dependency on: bzip2/1.0.8-GCCcore-10.3.0 cnpy/20180601-foss-2021a Eigen/3.3.9-GCCcore-10.3.0 foss/2021a GSL/2.7-GCC-10.3.0 NLopt/2.7.0-GCCcore-10.3.0 PCRE/8.44-GCCcore-10.3.0 RapidJSON/1.1.0-GCCcore-10.3.0 SAMtools/0.1.19-GCC-10.3.0 SQLite/3.35.4-GCCcore-10.3.0 tabix/0.2.6-GCCcore-10.3.0 zlib/1.2.11-GCCcore-10.3.0 zstd/1.4.9-GCCcore-10.3.0
Last modified on 5th December 2022