Command Line Options

You can obtain the complete list of options by running rvtest --help.

Basic Input/Output

            --inVcf : input VCF File
              --out : output prefix
        --outputRaw : Output genotypes, phenotype, covariates(if any) and
                      collapsed genotype to tabular files

Specify Covariate

            --covar : specify covariate file
       --covar-name : specify the column name in coavriate file to be
                      incluced in analysis
              --sex : Include sex (5th) as covaraite from PED file

Specify Phenotype

            --pheno : specify phenotype file
    --inverseNormal : transform phenotype like normal distribution
--useResidualAsPhenotype: fit covariate ~ phenotype, use residual to replace
                      phenotype
           --mpheno : specify which phenotype column to read (default: 1)
       --pheno-name : specify which phenotype column to read by header
              --qtl : treat phenotype as quantitative trait

Specify Genotype

           --dosage : Specify which dosage tag to use. (e.g. EC)

Chromsome X Options

           --xLabel : Specify X chromosome label (default: 23|X
       --xParRegion : Specify PAR region (default: hg19), can be build number
                      e.g. hg38, b37; or specify region, e.g.
                      '60001-2699520,154931044-155260560'

People Filter

  --peopleIncludeID : give IDs of people that will be included in study
--peopleIncludeFile : from given file, set IDs of people that will be
                      included in study
  --peopleExcludeID : give IDs of people that will be included in study
--peopleExcludeFile : from given file, set IDs of people that will be
                      included in study

Site Filter

        --rangeList : Specify some ranges to use, please use chr:begin-end
                      format.
        --rangeFile : Specify the file containing ranges, please use
                      chr:begin-end format.
         --siteFile : Specify the file containing sites to include, please
                      use "chr pos" format.
     --siteDepthMin : Specify minimum depth(inclusive) to be incluced in
                      analysis
     --siteDepthMax : Specify maximum depth(inclusive) to be incluced in
                      analysis
       --siteMACMin : Specify minimum Minor Allele Count(inclusive) to be
                      incluced in analysis
         --annoType : Specify annotation type that is follwed by ANNO= in the
                      VCF INFO field, regular expression is allowed

Genotype Filter

     --indvDepthMin : Specify minimum depth(inclusive) of a sample to be
                      incluced in analysis
     --indvDepthMax : Specify maximum depth(inclusive) of a sample to be
                      incluced in analysis
      --indvQualMin : Specify minimum depth(inclusive) of a sample to be
                      incluced in analysis

Association Model

           --single : score, wald, exact, famScore, famLrt, famGrammarGamma
           --burden : cmc, zeggini, mb, exactCMC, rarecover, cmat, cmcWald
               --vt : cmc, zeggini, mb, skat
           --kernel : SKAT, KBAC
             --meta : score, cov, dominant, recessive

Family-based Models

          --kinship : Specify a kinship file for autosomal analysis, use
                      vcf2kinship to generate
     --xHemiKinship : Provide kinship for the chromosome X hemizygote region

Grouping Unit

         --geneFile : specify a gene file (for burden tests)
             --gene : specify which genes to test
          --setList : specify a list to test (for burden tests)
          --setFile : specify a list file (for burden tests, first 2 columns:
                      setName chr:beg-end)
              --set : specify which set to test (1st column)

Frequency Cutoff

        --freqUpper : Specify upper frequency bound to be included in
                      analysis
        --freqLower : Specify lower frequency bound to be included in
                      analysis

Missing Data

           --impute : Impute missing genotype (default:mean):  mean, hwe, and
                      drop
      --imputePheno : Impute phenotype to mean of those have genotypes but no
                      phenotpyes
        --imputeCov : Impute each covariate to its mean, instead of drop
                      samples with missing covariates

Conditional Analysis

        --condition : Specify markers to be conditions (specify range)

Auxilliary Functions

             --help : Print detailed help message