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 : --kinGeno, --empMaf [0.05], --empMiss [0.05],
                             --outputX, --outputKin, --kinFile [],
                             --kinPrefix []
      Input/Output Options : --vcf [], --groupFile [], --freqFile [],
                             --prefix []
                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]
             Other Options : --function [], --mafMin [0.00], --mafMax [0.50],
                             --mac [0.00], --noStop, --xLabel [X],
                             --Xstart [2699520], --Xend [154931044], --dosage,
                             --founderFreq, --h2Only, --fullResult [ON]

Example Command Line

Single Variant Analysis

The following command gives let you run single variant association analysis of trait "LDL" using score test, after inverse normalization of the quantitative trait and adjusting covariates. --traitName specifies the single trait or traits you want to analyze in this batch. If this option is not used, then all traits coded in data file will be analyzed accordingly. --SingleVarLRT provides essentially the same test as in merlin --fastAssoc option.

./famRvTest -p your.ped -d your.dat --SingleVarScore --inverseNormal --useCovariates --traitName LDL

Futhermore, if you want to run likelihood ratio test and wald test at the same time, the following command should do the work:

./famRvTest -p your.ped -d your.dat --SingleVarScore --SingleVarLRT --SingleVarWald --inverseNormal --useCovariates --traitName LDL

All the above commands will let you do family-based association analysis using kinship matrices generated using pedigree structure coded in pedigree file. The following command lines show examples of using genotype to estimate empirical relationship matrix to do the work.

 ./famRvTest -p your.ped -d your.dat --SingleVarScore --SingleVarLRT --SingleVarWald --inverseNormal --useCovariates --traitName LDL --empKin