RAREFY DOCUMENTATION

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Revision as of 15:13, 3 February 2015 by Shuang Feng (talk | contribs) (SOFTWARE INTERFACE)
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KEY FEATURES

  • RAREFY is a likelihood-based method to prioritize individuals in family samples and population samples.
  • RAREFY takes account familial relatedness and allows adjusting covariates.
  • RAREFY is able to handle large and complex pedigrees.

INPUT FILE FORMAT

  • RAREFY takes MERLIN format PED/DAT files as input, no MAP file is needed.
  • Input files should have pedigree information, phenotype, and covariates information (if covariates are to be adjusted) saved.

SOFTWARE INTERFACE

Options:

   Input Files : --ped [], --dat []
      Methods : --MCMC, --traitIncreasing, --traitDecreasing
            Trait : --inverseNormal, --logTransform, --useCovariates,
                --traitName []
  Parameters : --maf [1.0e-03], --effect [2.00]
         MCMC : --seed, --chains [3], --iterations [50000000]
          Other : --famList [], --famID [], --cpus [5], --prefix []

EXAMPLES