FamRvTest command

                    Data File :                 (-dname)
                Pedigree File :                 (-pname)

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 : --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]

Crucial Input Files:

famRvTest takes Merlin format pedigree and data file as input. These two files are crucial for the program to run. Please refer to Merlin documentation for details.

Kinship Options:

--kinGeno allows you to estimate relationship matrix using genotypes; otherwise, kinship matrix based on pedigree structure will be used.
--empMaf and --empMiss specifies the cutoff of minor allele frequency and genotype missing rate to filter SNPs for estimating empirical kinship matrix.
--outputX allows you to save kinship matrix from chromosome X. 
--outputKin allows you to save the kinship matrix from autosomal matrix if --outputX is also specified.
--kinFile allows you to read kinship matrix from a previously saved file.
--kinPrefix specifies the file prefix for kinship matrices saved.

Input/Output Options:

--vcf specified the name of input vcf file.
--groupFile should be followed by a the name of the groupfile you want to use for gene-level associations.
--freqFile allows users to read allele frequencies from a file instead of estimating based on data.
--prefix specifies the name of file prefix for all results saved.

SingleVar Tests:

--SingleVarWald, --SingleVarScore and --SingleVarLRT are wald, score and likelihood ratio tests.

Burden Tests:

--SKAT --MB --CMC_binary --CMC_counts are SKAT, weighted-burden test (Madsen-Browning weight), collapsing burden test and unweighted burden test based on rare allele count.

VT Tests:

--VTasymptotic performs variable threshold test and calculate asymptotic p-value.
--VTpermute performs variable threshold test and calculate p-value based on permutation.
--permuteMin [1000] and --permuteMax [3000000] specify the min and max number of permutation.

Other Options:

--function allows grouping by functional annotation when annotated vcf file is used for gene-level association tests.
--mafMin [0.00] and --mafMax [0.50] specify the minimum and maximum allele frequency for variants to group. 
--mac [0.0] specify the minimum rare allele count as one of the filters to rare variants to group.
--noStop indicating no stopping rule to be used in VT permutation test.
--xLabel [X] specifies labels for chromosome X.
--Xstart [2699520] and --Xend [154931044] are start and end position of non-pseudo-autosomal region.
--founderFreq considers founder allele frequencies in analysis.
--h2Only provides a shortcut of calculating heritability only.
--fullResult [on] provides results in long format in gene-level association testing, including results from single markers included in analysis.