FamRvTest command: Difference between revisions

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==Overview of Options==
==Overview of Options==
 
                  Data File :                (-dname)
                Pedigree File :                (-pname)
   
   
Options:
Options:
            Kinship Options : --kinGeno, --empMaf [0.05], --empMiss [0.05],
        Kinship Options : --kinGeno, --kinPedigree, --kinFile [], --kinSave,
                              --outputX, --outputKin, --kinFile [],
                          --kinMaf [0.05], --kinMiss [0.05]
                              --kinPrefix []
  Input/Output Options : --ped [], --dat [], --vcf [], --noeof,
      Input/Output Options : --vcf [], --groupFile [], --freqFile [],
                          --groupFile [], --longOutput [ON], --prefix []
                              --prefix []
            VC Options : --inverseNormal, --useCovariates, --traitName []
                VC Options : --inverseNormal, --fitSharedEnv, --fitX,
  Single Variant Tests : --SingleVarScore
                              --useCovariates, --traitName []
          Burden Tests : --burden, --MB, --VT, --SKAT_BETA, --SKAT_UW,
            SingleVar Tests : --SingleVarLRT, --SingleVarScore,
                          --SKAT_MB
                              --SingleVarWald
          Other Options : --freqFile [], --annotation [], --maf [0.05],
              Burden Tests : --SKAT, --MB, --CMC_binary, --CMC_counts
                          --miss [0.05], --simulate, --dosage, --founderFreq
  Variable Threshold Tests : --VTasymptotic, --VTpermute, --permuteMin [1000],
              PhoneHome : --noPhoneHome, --phoneHomeThinning [100]
                              --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===
===Kinship Options ===
'''famRvTest''' takes Merlin format pedigree and data file as input. These two files are crucial for the program to run. Please refer to [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html|'''Merlin'''] documentation for details.
--kinGeno: kinship matrix is estimated from genotype
===Kinship Options===
 
--kinGeno allows you to estimate relationship matrix using genotypes; otherwise, kinship matrix based on pedigree structure will be used.
--kinPedigree: kinship matrix is estimated from pedigree structure
--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.
--kinFile: kinship matrix is read from a file
--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.
--kinMaf: the maf cutoff for markers used to estimate kinship
--kinPrefix specifies the file prefix for kinship matrices saved.
 
--kinMiss: the genotype call rate cutoff for markers included to estimate kinship


===Input/Output Options===
===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===
--ped: merlin format ped file.
--SingleVarWald, --SingleVarScore and --SingleVarLRT are wald, score and likelihood ratio tests.
 
--dat: merlin format dat file.
 
--vcf: vcf file
 
--groupFile: gene group file for gene level tests
 
--longOutput: [ON/OFF] turning this option on will include single variants results in gene-level results report also.
 
--prefix: output file prefix
 
===VC options===
 
--inverseNormal: trait will be inverse normalized before analysis
 
--useCovariates: covariates saved in ped file will be adjusted
 
--traitName: a specified trait that needs to be analyzed. If not specified, then all traits will be analyzed.
 
 
===  Single Variant Tests===
 
--SingleVarScore: the score test


===Burden 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===
--burden: the unweighted burden test
--VTasymptotic performs variable threshold test and calculate asymptotic p-value.
 
--VTpermute performs variable threshold test and calculate p-value based on permutation.
--MB: the Madsen-Browning weighted burden test
--permuteMin [1000] and --permuteMax [3000000] specify the min and max number of permutation.
 
--VT: the variable threshold test
 
--SKAT_BETA: the beta density weighted SKAT test (the original test)
 
--SKAT_UW: the unweighted SKAT test
 
--SKAT_MB: the Madsen-Browning weighted SKAT test
 


===Other Options===
===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.
--freqFile []: allow users to enter frequency of markers from a file
--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.
--annotation: allow users to group variants based on annotation
--xLabel [X] specifies labels for chromosome X.
 
--Xstart [2699520] and --Xend [154931044] are start and end position of non-pseudo-autosomal region.
--maf: maf cutoff for markers to be grouped for gene-level tests
--founderFreq considers founder allele frequencies in analysis.
 
--h2Only provides a shortcut of calculating heritability only.
--miss: the genotype calling missing rate filter before grouping variants for gene-level tests
--fullResult [on] provides results in long format in gene-level association testing, including results from single markers included in analysis.
 
--simulate: allows an integer for number of permutations requested in single variant score test
 
--dosage: the flag to tell use dosage saved in VCF file, instead of genotype
 
--founderFreq: use founder frequencies for grouping and weighting

Latest revision as of 01:48, 14 July 2014

Useful Pages

famRvTest Home Page

famRvTest Tutorial

Overview of Options

Options: 

       Kinship Options : --kinGeno, --kinPedigree, --kinFile [], --kinSave,
                         --kinMaf [0.05], --kinMiss [0.05]
  Input/Output Options : --ped [], --dat [], --vcf [], --noeof,
                         --groupFile [], --longOutput [ON], --prefix []
            VC Options : --inverseNormal, --useCovariates, --traitName []
  Single Variant Tests : --SingleVarScore
          Burden Tests : --burden, --MB, --VT, --SKAT_BETA, --SKAT_UW,
                         --SKAT_MB
         Other Options : --freqFile [], --annotation [], --maf [0.05],
                         --miss [0.05], --simulate, --dosage, --founderFreq
             PhoneHome : --noPhoneHome, --phoneHomeThinning [100]

Kinship Options

--kinGeno: kinship matrix is estimated from genotype

--kinPedigree: kinship matrix is estimated from pedigree structure

--kinFile: kinship matrix is read from a file

--kinMaf: the maf cutoff for markers used to estimate kinship

--kinMiss: the genotype call rate cutoff for markers included to estimate kinship

Input/Output Options

--ped: merlin format ped file.

--dat: merlin format dat file.

--vcf: vcf file

--groupFile: gene group file for gene level tests

--longOutput: [ON/OFF] turning this option on will include single variants results in gene-level results report also.

--prefix: output file prefix

VC options

--inverseNormal: trait will be inverse normalized before analysis

--useCovariates: covariates saved in ped file will be adjusted

--traitName: a specified trait that needs to be analyzed. If not specified, then all traits will be analyzed.


Single Variant Tests

--SingleVarScore: the score test

Burden Tests

--burden: the unweighted burden test

--MB: the Madsen-Browning weighted burden test

--VT: the variable threshold test

--SKAT_BETA: the beta density weighted SKAT test (the original test)

--SKAT_UW: the unweighted SKAT test

--SKAT_MB: the Madsen-Browning weighted SKAT test


Other Options

--freqFile []: allow users to enter frequency of markers from a file

--annotation: allow users to group variants based on annotation

--maf: maf cutoff for markers to be grouped for gene-level tests

--miss: the genotype calling missing rate filter before grouping variants for gene-level tests

--simulate: allows an integer for number of permutations requested in single variant score test

--dosage: the flag to tell use dosage saved in VCF file, instead of genotype

--founderFreq: use founder frequencies for grouping and weighting

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