RAREFY DOCUMENTATION

Useful Wiki Pages

• The RAREFY Home
• The RAREFY Download Page
• The RAREFY Command Reference
• The RAREFY Tutorial
• The FAQ

KEY FEATURES

• RAREFY is a likelihood-based method to prioritize individuals in family AND population samples.

• RAREFY takes account familial relatedness and allows adjusting covariates.

• RAREFY is able to handle large and complex pedigrees.

DOWNLOAD & BUILD

Please go to DOWNLOAD PAGE for source code and executables.

INPUT 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.

OUTPUT FORMAT

RAREFY generates output file with eight columns.

SOFTWARE INTERFACE

Options:
  Input Files : --ped [], --dat []
      Methods : --MCMC, --traitIncreasing, --traitDecreasing
        Trait : --inverseNormal, --useCovariates, --traitName []
   Parameters : --maf [1.0e-03], --effect [1.00]
         MCMC : --seed, --chains [3], --iterations [50000000]
        Other : --famList [], --famID [], --cpus [5], --prefix []

Please see RAREFY COMMAND REFERENCE for detailed description of usage, and EXAMPLES for quick examples.

EXAMPLES

• To prioritize individuals likely to be carriers of trait-increasing rare variants:

rarefy --ped your.ped --dat your.dat --traitIncreasing --prefix your.output.prefix

• To prioritize individuals likely to be carriers of trait-decreasing rare variants:

rarefy --ped your.ped --dat your.dat --traitDecreasing --prefix your.output.prefix

• To prioritize individuals likely to be carriers of either trait-decreasing or trait-decreasing rare variants:

rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --prefix your.output.prefix

• To analyze families using MCMC method in 3 chains and 50000000 iterations:

rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --MCMC --chains 3 --iterations 50000000 --prefix your.output.prefix

• To inverse Normalize the phenotype before analysis:

rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --inverseNormal --prefix your.output.prefix 

• To inverse Normalize the phenotype and then adjust covariates saved in PED/DAT file before RAREFY analysis:

rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --inverseNormal --useCovariates --prefix your.output.prefix

• To analyze only a subset of families in the sample:

rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --famList your.file.with.famID --prefix your.output.prefix 
NOTE: although only the subset of families will be "RAREFIED", all samples saved in your.ped will be used to fit variance component model.

• To analyze only one family:

rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --famID fam123 --prefix your.output.prefix
NOTE: although only the family included in --famID will be "RAREFIED", all samples saved in your.ped will be used to fit variance component model.

• To analyze only one trait saved in your.ped and your.dat file:

rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --traitName LDL --prefix your.output.prefix