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| + | [[Category:RAREMETALWORKER]] |
| ==Useful Links== | | ==Useful Links== |
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| | | |
| Options: | | Options: |
− | Input Files : --ped [], --dat [], --vcf [], --dosage, --noeof | + | Input Files : --ped [], --dat [], --vcf [], --dosage, --flagDosage [DS], |
| + | --noeof |
| Output Files : --prefix [], --LDwindow [1000000], --zip, --thin, | | Output Files : --prefix [], --LDwindow [1000000], --zip, --thin, |
| --labelHits | | --labelHits |
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| --maleLabel [1], --femaleLabel [2] | | --maleLabel [1], --femaleLabel [2] |
| others : --cpu [1], --kinOnly, | | others : --cpu [1], --kinOnly, |
− | --geneMap [../data/refFlat_hg19.txt] | + | --geneMap [../data/refFlat_hg19.txt], --mergedVCFID |
| PhoneHome : --noPhoneHome, --phoneHomeThinning [100] | | PhoneHome : --noPhoneHome, --phoneHomeThinning [100] |
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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. |
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| === --thin === | | === --thin === |
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| * --geneMap takes a string describing the path to find mapping file for manhattan plot annotation. | | * --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. | | * 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. |
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| ==PhoneHome== | | ==PhoneHome== |