FamRvTest command

Useful Pages

famRvTest Home Page

famRvTest Tutorial

Overview of Options

                  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.