RAREFY DOCUMENTATION
From Genome Analysis Wiki
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 []
