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| + | [[Category:RAREMETALWORKER]] |
| ==Useful Links== | | ==Useful Links== |
| | | |
| Here are some useful links to key pages: | | Here are some useful links to key pages: |
− | * [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']] | + | * The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']] |
− | * [[RAREMETALWORKER_METHOD | '''RAREMETALWORKER method''']] | + | * The [[RAREMETALWORKER_METHOD | '''RAREMETALWORKER method''']] |
− | * [[RAREMETALWORKER_SPECIAL_TOPICS | '''RAREMETALWORKER special topics''']] | + | * The [[RAREMETALWORKER_SPECIAL_TOPICS | '''RAREMETALWORKER special topics''']] |
− | * [[Tutorial:_RAREMETAL | '''RAREMETALWORKER quick start tutorial''']] | + | * The [[Tutorial:_RAREMETAL | '''RAREMETALWORKER quick start tutorial''']] |
− | * [[RAREMETAL_FAQ | '''FAQ''']] | + | * The [[RAREMETAL_FAQ | '''FAQ''']] |
| | | |
− | ==List of Options ==
| + | Options: |
− | | + | Input Files : --ped [], --dat [], --vcf [], --dosage, --flagDosage [DS], |
− | Options:
| + | --noeof |
− | Input Files : --ped [], --dat [], --vcf [], --dosage, --noeof
| + | Output Files : --prefix [], --LDwindow [1000000], --zip, --thin, |
− | Output Files : --prefix [], --LDwindow [1000000], --zip, --thin,
| + | --labelHits |
− | --labelHits
| + | VC Options : --vcX, --separateX |
− | VC Options : --vcX, --separateX
| + | Trait Options : --makeResiduals, --inverseNormal, --traitName [] |
− | Trait Options : --makeResiduals, --inverseNormal, --traitName []
| + | Model Options : --recessive, --dominant |
− | Model Options : --recessive, --dominant
| + | Kinship Source : --kinPedigree, --kinGeno, --kinFile [], --kinxFile [], |
− | Kinship Source : --kinPedigree, --kinGeno, --kinFile [], --kinxFile [],
| + | --kinSave |
− | --kinSave
| + | Kinship Options : --kinMaf [0.05], --kinMiss [0.05] |
− | Kinship Options : --kinMaf [0.05], --kinMiss [0.05]
| + | Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044], |
− | Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044],
| + | --maleLabel [1], --femaleLabel [2] |
− | --maleLabel [1], --femaleLabel [2]
| + | others : --cpu [1], --kinOnly, |
− | PhoneHome : --noPhoneHome, --phoneHomeThinning [100]
| + | --geneMap [../data/refFlat_hg19.txt], --mergedVCFID |
| + | PhoneHome : --noPhoneHome, --phoneHomeThinning [100] |
| | | |
| ==Input Files== | | ==Input Files== |
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| * --dosage must be used with --vcf option. | | * --dosage must be used with --vcf option. |
| * Description of dosage format in a VCF file can be found in [[RAREMETALWORKER#DOSAGE | '''dosage''']]. | | * Description of dosage format in a VCF file can be found in [[RAREMETALWORKER#DOSAGE | '''dosage''']]. |
| + | |
| + | ===--flagDosage=== |
| + | * This option let user customize the name of field in VCF file that labels dosage data. |
| + | * The default is "DS". |
| + | |
| ===--noeof=== | | ===--noeof=== |
| * If you VCF file does not have the BGZF EOF markers, you should use --noeof option to let RAREMETALWORKER skip checking the BGZF EOF markers at the end of the file. | | * If you VCF file does not have the BGZF EOF markers, you should use --noeof option to let RAREMETALWORKER skip checking the BGZF EOF markers at the end of the file. |
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| | | |
| ===--zip=== | | ===--zip=== |
− | * By issuing --zip, RAREMETALWORKER compress the [[ RAREMETALWORKER#Summary_Statistics| '''summary statistics''']] and [[RAREMETALWORKER#LD_Matrices | '''LD matrices''']] generated automatically, using gzip. | + | * By issuing --zip, RAREMETALWORKER compress the [[ RAREMETALWORKER#Summary_Statistics| '''summary statistics''']] and [[RAREMETALWORKER#LD_Matrices | '''LD matrices''']] generated automatically, using gzip. And the output zip files will be indexed using tabix. |
| | | |
| === --thin === | | === --thin === |
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| * --xStart takes an integer that described the end position of nonPAR region on chromosome X. | | * --xStart takes an integer that described the end position of nonPAR region on chromosome X. |
| * The default is 154931044 based on Human Genome build 19. | | * The default is 154931044 based on Human Genome build 19. |
| + | |
| + | ==Others== |
| + | ===--cpu[1]=== |
| + | *--cpu takes an integer that specifies the number of cpus to use for estimating kinship matrix from genotypes. |
| + | |
| + | ===--kinOnly=== |
| + | *--kinOnly allows users to estimate kinship matrix without any association analysis of any traits included in the data set. |
| + | *To also estimate chromosome X kinship, --vcX option should be added in command line. |
| + | |
| + | ===--geneMap=== |
| + | * --geneMap takes a string describing the path to find mapping file for manhattan plot annotation. |
| + | * The default is human genome build 19, saved in raremetal/data/refFlat_hg19.txt. |
| + | |
| + | ===--mergedVCFID=== |
| + | * This options allows RAREMETALWORKER to recognize VCF samples IDs in "FAMID_PID" format. |
| + | * The default value is OFF, which means VCF sample IDs are consistent with PID field in PED file. |
| | | |
| ==PhoneHome== | | ==PhoneHome== |