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/BGEN/PLINK format as genotype input file and takes PLINK format phenotype file and covariate file.

References:

• Xiaowei Zhan, et al. RVTESTS: An Efficient and Comprehensive Tool for Rare Variant Association Analysis Using Sequence Data. Bioinformatics 2016 32: 1423-1426. doi:10.1093/bioinformatics/btw079

• Rvtests Main Site

• Module Name: rvtests (see the modules page for more information)
• singlethreaded
• Example files in /usr/local/apps/rvtests/2.0.6/example/

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load rvtests

[user@cn3144 ~]$ RV_DIR=/usr/local/apps/rvtests/2.0.6/example/

[user@cn3144 ~]$ rvtest --inVcf $RV_DIR/example.vcf --pheno $RV_DIR/pheno --out output --single wald,score
Thank you for using rvtests (version: 20171009, git: Unknown)
  For documentations, refer to http://zhanxw.github.io/rvtests/
  For questions and comments, send to Xiaowei Zhan 
  For bugs and feature requests, please submit at: https://github.com/zhanxw/rvtests/issues
[...]
[INFO]	Analysis begins with [ 9 ] samples...
[INFO]	Impute missing genotype to mean (by default)
[INFO]	Analysis started
[INFO]	Analyzed [ 3 ] variants
[INFO]	Analysis ends at: Mon Apr  9 11:50:48 2018
[INFO]	Analysis took 2 seconds
RVTESTS finished successfully

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. rvtests.sh). For example:

#!/bin/bash
set -e
module load rvtests
RV_DIR=/usr/local/apps/rvtests/2.0.6/example/
rvtest --inVcf $RV_DIR/example.vcf --pheno $RV_DIR/pheno --out output --single wald,score

Submit this job using the Slurm sbatch command.

sbatch rvtests.sh

Create a swarmfile (e.g. rvtests.swarm). For example:

rvtest --inVcf example.1vcf --pheno pheno1 --out output1 --single wald,score
rvtest --inVcf example.2vcf --pheno pheno2 --out output2 --single wald,score
rvtest --inVcf example.3vcf --pheno pheno3 --out output3 --single wald,score

Submit this job using the swarm command.

swarm -f rvtests.swarm --module rvtests