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FamRvTest command

Revision as of 01:48, 14 July 2014 by Shuang Feng (talk | contribs) (Overview of Options)
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Useful Pages

Overview of 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,
         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