Line 1: |
Line 1: |
| + | == Useful Wiki Pages == |
| + | |
| + | * The [[RAREFY | '''RAREFY Home''']] |
| + | * The [[RAREFY_DOWNLOAD | '''RAREFY Download Page''']] |
| + | * The [[RAREFY_COMMAND | '''RAREFY Command Reference''']] |
| + | * The [[RAREFY_TUTORIAL | '''RAREFY Tutorial''']] |
| + | * The [[RAREFY_FAQ | '''FAQ''']] |
| + | |
| ==KEY FEATURES== | | ==KEY FEATURES== |
| | | |
Line 7: |
Line 15: |
| *'''RAREFY''' is able to handle large and complex pedigrees. | | *'''RAREFY''' is able to handle large and complex pedigrees. |
| | | |
− | ==INPUT FILE FORMAT== | + | ==DOWNLOAD & BUILD== |
| + | Please go to [[RAREFY_DOWNLOAD | '''DOWNLOAD PAGE''']] for source code and executables. |
| + | |
| + | ==INPUT FORMAT== |
| *'''RAREFY''' takes [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED/DAT files] as input, no MAP file is needed. | | *'''RAREFY''' takes [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html 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. | | *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== | | ==SOFTWARE INTERFACE== |
Line 20: |
Line 34: |
| MCMC : --seed, --chains [3], --iterations [50000000] | | MCMC : --seed, --chains [3], --iterations [50000000] |
| Other : --famList [], --famID [], --cpus [5], --prefix [] | | Other : --famList [], --famID [], --cpus [5], --prefix [] |
| + | |
| + | Please see [[RAREFY_COMMAND| '''RAREFY COMMAND REFERENCE''']] for detailed description of usage, and [[RAREFY_DOC#EXAMPLES | '''EXAMPLES''']] for quick examples. |
| | | |
| ==EXAMPLES== | | ==EXAMPLES== |
Line 27: |
Line 43: |
| rarefy --ped your.ped --dat your.dat --traitDecreasing --prefix your.output.prefix | | 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: | | *To prioritize individuals likely to be carriers of either trait-decreasing or trait-decreasing rare variants: |
− | rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --prefix your.output.prefix | + | 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: | | *To analyze families using MCMC method in 3 chains and 50000000 iterations: |
− | rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --MCMC --chains 3 --iterations 50000000 --prefix your.output.prefix | + | 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: | | *To inverse Normalize the phenotype before analysis: |
− | rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --inverseNormal --prefix your.output.prefix | + | 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: | | *To analyze only a subset of families in the sample: |
− | rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --famList your.file.with.famID --prefix your.output.prefix | + | 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: | | *To analyze only one family: |
− | rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --famID fam123 --prefix your.output.prefix | + | 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 |