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Revision as of 17:47, 16 March 2018
, 17:47, 16 March 2018no edit summary
[[Category:RAREMETALWORKER]]
==Useful Links==
==Useful Links==
* The [[RAREMETAL_FAQ | '''FAQ''']]
* The [[RAREMETAL_FAQ | '''FAQ''']]
Options:
Input Files : --ped [], --dat [], --vcf [], --dosage, --flagDosage [DS],
--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]
others : --cpu [1], --kinOnly,
--geneMap [../data/refFlat_hg19.txt], --mergedVCFID
PhoneHome : --noPhoneHome, --phoneHomeThinning [100]
==Input Files==
==Input Files==
* --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.
===--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 ===
* --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==
