Changes

'''RAREMETALWORKER''' is a tool for single variant analysis, generating summary statistics for gene level meta analyses in [http://genome.sph.umich.edu/wiki/RAREMETAL '''RAREMETAL'''].

'''RAREMETALWORKER''' is a tool for single variant analysis, generating summary statistics for gene level meta analyses in [http://genome.sph.umich.edu/wiki/RAREMETAL '''RAREMETAL'''].

If you feel this program is useful, please tell us your name and contact in this [https://docs.google.com/spreadsheet/ccc?key=0AuYjznTeEDYudFpqUk9sQ2pkN3d3endjYldqMEp6ZUE&usp=sharing '''registration'''].

If you feel this program is useful, please tell us your name and contact in this [https://docs.google.com/spreadsheet/ccc?key=0AuYjznTeEDYudFpqUk9sQ2pkN3d3endjYldqMEp6ZUE&usp=sharing '''registration'''].

If you have any questions, please contact [[Shuang Feng|'''Shuang Feng''']] sfengsph at umich dot edu or [[Goncalo_Abecasis | '''Goncalo Abecasis''']] goncalo at umich dot edu.

If you have any questions, please contact Sai Chen (saichen at umich dot edu) or [[Goncalo_Abecasis | '''Goncalo Abecasis''']] (goncalo at umich dot edu).

* The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]

* The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]

* The [[RAREMETAL FAQ | '''FAQ''']]

* The [[RAREMETAL FAQ | '''FAQ''']]

== Key Features ==

== Key Features ==

* '''Markers in PED and DAT file must be sorted by chromosome and position.'''

* '''Markers in PED and DAT file must be sorted by chromosome and position.'''

* Covariate and trait values are saved in PED file. Covariate and trait descriptions are saved in DAT file.

* Covariate and trait values are saved in PED file. Covariate and trait descriptions are saved in DAT file. Note that you must specify <code>--makeResiduals</code> in order to adjust the covariates out of the phenotype. See [[RAREMETALWORKER#Example_Command_Lines | Example Command Lines]] for examples and [[RAREMETALWORKER_command_reference#Trait_Options | Trait Options]] for more information.

==== VCF File ====

==== VCF File ====

* If --zip option is used, then the following will be generated automatically:

* If --zip option is used, then the following will be generated automatically:

   prefix.traitName.singlevar.score.txt.gz

   prefix.traitName.singlevar.score.txt.gz

   prefix.traitName.singlevar.cov.txt.gz

   prefix.traitName.singlevar.cov.txt.gz

   prefix.singlevar.log

   prefix.singlevar.log