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, BEARCloud VMs, and CaStLeS VMs):
module load Rvtests/2.1.0-foss-2021a
BEAR Apps Version
The listed architectures consist of two part: OS-CPU.
- BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
- BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.
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