From Genome Analysis Wiki
Jump to navigationJump to search
1,783 bytes added
, 12:12, 14 April 2014
Line 1: |
Line 1: |
− | ==== 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: |