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From Genome Analysis Wiki
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== Useful Wiki Pages ==
* The [[RAREFY | '''RAREFY Home''']]
* The [[RAREFY_DOC | '''RAREFY Documentation''']]
* The [[RAREFY_TUTORIAL | '''RAREFY Tutorial''']]
* The [[RAREFY_DOWNLOAD | '''RAREFY Download Page''']]
* The [[RAREFY_FAQ | '''FAQ''']]
==RAREFY COMMANDS==
Options:
Options:
Input Files : --ped [], --dat []
Input Files : --ped [], --dat []
==Input Files==
==Input Files==
===--ped [string]===
===--ped [string]===
followed by the file name of your[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED] file.
followed by the file name of your [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED] file.
===--dat [string]===
===--dat [string]===
==MCMC==
==MCMC==
===--seed [double]===
===--seed [int]===
===--chains [int]===
===--chains [int]===
The default is '''3'''. This options allows users to specify number of MCMC chains to run with different starting point. In general, less than 10 chains is recommended. The result is averaged over all chains.
The default is '''3'''. This options allows users to specify number of MCMC chains to run with different starting point. In general, less than 10 chains is recommended. The result is averaged over all chains.
