Famrvtest
From Genome Analysis Wiki
Brief Description
famRvTest is a computationally efficient tool for family-based association analyses of rare variants using sequencing or genotyping array data. famRvTest supports both single variant and gene-level associations.
Download and Installation
- University of Michigan CSG users can go to the following:
/net/fantasia/home/sfengsph/code/famRV/bin/famRvTesst
Where to Download
- The software package for Linux and Mac (source code included) can be downloaded here: software package download
How to Compile
- Save it to your local path and decompress using the following command:
tar xvzf FamRV.0.0.1.tgz
- Go to FamRV_0.0.1/famRvTest/src and type the following command to compile:
make
How to Execute
- Go to FamRV_0.0.1/famRvTest/bin and use the following:
./famRvTest
Approach
famRvTest uses linear mixed model approach to account for familial relationship, where kinship is either quantified based upon pedigree structures or estimated from genotypes of markers from genome-wide. Single marker associations including score, likelihood ratio and ward tests and gene-level associations methods (weighted and un-weighted burden, SKAT and variable threshold) have been implemented. Manuscript is under preparation.
Command References
Options: Kinship Options : --empKin, --empMaf [0.05], --empMiss [0.05], --outputX, --outputKin, --kinFile [], --prefix [] Input/Output Options : --vcf [], --groupFile [], --freqFile [], --outPrefix [] VC Options : --inverseNormal, --fitSharedEnv, --fitX, --useCovariates, --traitName [] SingleVar Tests : --SingleVarLRT, --SingleVarScore, --SingleVarWald Burden Tests : --Burden, --SKAT, --MB, --CMC_binary, --CMC_counts Variable Threshold Tests : --VTasymptotic, --VTpermute, --permuteMin [1000], --permuteMax [3000000], --VTMB, --VTCMC_binary, --VTCMC_counts [ON] Other Options : --function [], --mafMin [0.00], --mafMax [0.50], --mac [0.00], --noStop, --maleLabel [1], --femaleLabel [2], --xLabel [X], --Xstart [2699520], --Xend [154931044], --dosage, --founderFreq, --h2Only, --fullResult [ON]