Famrvtest

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]