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Revision as of 12:12, 14 April 2014
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==== Output Files ====
==Useful Links==
Here are some useful links to key pages:
* [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]
* [[RAREMETALWORKER_METHOD | '''RAREMETALWORKER method''']]
* [[RAREMETALWORKER_command_reference | '''RAREMETALWORKER command reference''']]
* [[RAREMETAL_FAQ | '''FAQ''']]
==List of Options ==
Options:
Input Files : --ped [], --dat [], --vcf [], --dosage, --noeof
Output Files : --prefix [], --LDwindow [1000000], --zip, --thin,
--labelHits
VC Options : --vcX, --separateX
Trait Options : --makeResiduals, --inverseNormal, --traitName []
Model Options : --recessive, --dominant
Kinship Source : --kinPedigree, --kinGeno, --kinFile [], --kinxFile [],
--kinSave
Kinship Options : --kinMaf [0.05], --kinMiss [0.05]
Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044],
--maleLabel [1], --femaleLabel [2]
PhoneHome : --noPhoneHome, --phoneHomeThinning [100]
==Input Files==
===--ped===
*--ped takes a string of your [[RAREMETALWORKER#PED_and_DAT_Files | '''MERLIN format PED''']] file name.
===--dat===
*--ped takes a string of your [[RAREMETALWORKER#PED_and_DAT_Files | '''MERLIN format DAT''']] file name.
===--vcf===
*--vcf takes a string of your [[RAREMETALWORKER#VCF_File | '''VCF''']] file name.
===--dosage===
* When --dosage is issued in command line, RAREMETALWORKER reads dosage from your [[RAREMETALWORKER#VCF_File | '''VCF''']] file.
* --dosage must be used with --vcf option.
* Description of dosage format can be found in [[RAREMETALWORKER#DOSAGE | '''DOSAGE''']].
===--noeof===
==Output Files==
==VC Options==
==Trait Options==
==Model Options==
==Kinship Source==
==Kinship Options=
==Chromosome X==
==PhoneHome==
* --prefix is optional.
* --prefix is optional.
* If --prefix is not specified, the output file names will be:
* If --prefix is not specified, the output file names will be:
