Difference between revisions of "RAREFY DOCUMENTATION"
From Genome Analysis Wiki
Jump to navigationJump to searchShuang Feng (talk | contribs) |
Shuang Feng (talk | contribs) |
||
Line 16: | Line 16: | ||
Input Files : --ped [], --dat [] | Input Files : --ped [], --dat [] | ||
Methods : --MCMC, --traitIncreasing, --traitDecreasing | Methods : --MCMC, --traitIncreasing, --traitDecreasing | ||
− | Trait : --inverseNormal | + | Trait : --inverseNormal, --useCovariates, --traitName [] |
− | + | Parameters : --maf [1.0e-03], --effect [1.00] | |
− | Parameters : --maf [1.0e-03], --effect [ | ||
MCMC : --seed, --chains [3], --iterations [50000000] | MCMC : --seed, --chains [3], --iterations [50000000] | ||
Other : --famList [], --famID [], --cpus [5], --prefix [] | Other : --famList [], --famID [], --cpus [5], --prefix [] | ||
==EXAMPLES== | ==EXAMPLES== |
Revision as of 15:15, 3 February 2015
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, --useCovariates, --traitName [] Parameters : --maf [1.0e-03], --effect [1.00] MCMC : --seed, --chains [3], --iterations [50000000] Other : --famList [], --famID [], --cpus [5], --prefix []