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RAREMETALWORKER command reference (view source)

Revision as of 17:47, 16 March 2018

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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:
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* [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]
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* The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]
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* [[RAREMETALWORKER_METHOD | '''RAREMETALWORKER method''']]
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* The [[RAREMETALWORKER_METHOD | '''RAREMETALWORKER method''']]
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* [[RAREMETALWORKER_SPECIAL_TOPICS | '''RAREMETALWORKER special topics''']]
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* The [[RAREMETALWORKER_SPECIAL_TOPICS | '''RAREMETALWORKER special topics''']]
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* [[RAREMETAL_FAQ | '''FAQ''']]
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* The [[Tutorial:_RAREMETAL | '''RAREMETALWORKER quick start tutorial''']]
 +
* The [[RAREMETAL_FAQ | '''FAQ''']]
   −
==List of Options ==
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Options:
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      Input Files : --ped [], --dat [], --vcf [], --dosage, --flagDosage [DS],
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  Options:
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                    --noeof
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        Input Files : --ped [], --dat [], --vcf [], --dosage, --noeof
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      Output Files : --prefix [], --LDwindow [1000000], --zip, --thin,
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      Output Files : --prefix [], --LDwindow [1000000], --zip, --thin,
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                    --labelHits
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                      --labelHits
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        VC Options : --vcX, --separateX
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        VC Options : --vcX, --separateX
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    Trait Options : --makeResiduals, --inverseNormal, --traitName []
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      Trait Options : --makeResiduals, --inverseNormal, --traitName []
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    Model Options : --recessive, --dominant
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      Model Options : --recessive, --dominant
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    Kinship Source : --kinPedigree, --kinGeno, --kinFile [], --kinxFile [],
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    Kinship Source : --kinPedigree, --kinGeno, --kinFile [], --kinxFile [],
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                    --kinSave
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                      --kinSave
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  Kinship Options : --kinMaf [0.05], --kinMiss [0.05]
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    Kinship Options : --kinMaf [0.05], --kinMiss [0.05]
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      Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044],
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      Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044],
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                    --maleLabel [1], --femaleLabel [2]
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                      --maleLabel [1], --femaleLabel [2]
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            others : --cpu [1], --kinOnly,
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          PhoneHome : --noPhoneHome, --phoneHomeThinning [100]
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                    --geneMap [../data/refFlat_hg19.txt], --mergedVCFID
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        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===
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* By issuing --zip, RAREMETALWORKER compress the [[ RAREMETALWORKER#Summary_Statistics| '''summary statistics''']] and [[RAREMETALWORKER#LD_Matrices | '''LD matrices''']] generated automatically, using gzip.  
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* 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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* The default is 154931044 based on Human Genome build 19.
 
* The default is 154931044 based on Human Genome build 19.
   −
==PhoneHome==
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==Others==
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===--noPhoneHome===
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===--cpu[1]===  
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===--phoneHomeThinning===
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*--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.
   −
* --prefix is optional.
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===--mergedVCFID===
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* If --prefix is not specified, the output file names will be:
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* This options allows RAREMETALWORKER to recognize VCF samples IDs in "FAMID_PID" format.  
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  traitname.singlevar.score.txt
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* The default value is OFF, which means VCF sample IDs are consistent with PID field in PED file.
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  traitname.singlevar.cov.txt
  −
* Otherwise, the output file names are:
  −
  prefix.traitname.singlevar.score.txt
  −
  prefix.traitname.singlevar.cov.txt
  −
* --LDwindow specifies the length of the window that LD Matrix should be generated upon each variant. The default is 1MB.
  −
* --zip gives users the option of writing compressed files (bgzip compressed) automatically for convenient sharing.
  −
* --thin tells RMW to thin points when generating QQ plot and Manhattan plots, so the file size is smaller.
  −
* --labelHits tells RMW to to label the hits using pvalue threshold 0.05/(#of variants tested) with gene name, based on human genome build 19.
     −
==== VC Options ====
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==PhoneHome==
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* When --vcShared and --vcX are specified, RMW knows that you want to fit shared environment and/or chromosome X variance component together with genetic component and non-shared environment.
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* See [[PhoneHome]] for more information on how PhoneHome works and what it does.
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* When --makeResiduals is specified, RMW understands covariates should be read from PED/DAT file. Covariates are modeled as fixed effects.
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===--noPhoneHome===
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* --noPhoneHome disables PhoneHome.  
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==== Trait Options ====
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* PhoneHome is enabled by default based on the thinning parameter.
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* --makeResiduals tells RMW to adjust the covariates and analyze residuals instead of the original phenotypes. If either --kinGeno or --kinPedigree option is used, then a variance component model will be fit based on residuals. If the --inverseNormal option is also used, then the residuals will be quantile normalized before fitting variance component model.
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===--phoneHomeThinning===
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* --traitName is created for situations when you have many traits saved in your PED and DAT file, but you are interested in one or a few of them. It can read a file ending with .txt with each trait of interest in a separate line, or trait names separated with "/". An example to handle one trait or multiple traits is in the following:
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* --phoneHomeThinning (0-100) adjusts the frequency of PhoneHome.
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  --traitName LDL
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* The default is 100, running 100% of the time.
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  --traitName LDL/HDL/TG
  −
  --traitName traitsOfInterest.txt
  −
* If --traitName is not used, all traits in PED/DAT file will be analyzed.
  −
 
  −
==== Model Options ====
  −
* additive model is used in RMW as default.
  −
* --recessive allows additional association results (pvalue, effect size, and standard error) generated using recessive model. If VCF file is used, then non-reference allele is considered the recessive allele. If PED/DAT files are used for genotype, then minor allele is considered the recessive allele.  
  −
* --dominant allows additional association results (pvalue, effect size, and standard error) generated using dominant model. If VCF file is used, then non-reference allele is considered the dominant allele. If PED/DAT files are used for genotype, then minor allele is considered the dominant allele.
  −
* --recessive and --dominant options can be used together.
  −
* Recessive and dominant results are stored in separate files.
  −
 
  −
==== Kinship Source ====
  −
* --kinPedigree allows RMW to generate kinship matrix from pedigree, when pedigree information is available.
  −
* --kinGeno informs RMW to generate kinship matrix from all available variants that pass the criteria, specified in --kinMaf and --kinMiss options. The default will take variants with MAF>0.05 and genotype missing rate <0.05.
  −
* --kinGeno option can NOT be used with --kinPedigree or --kinFile option. Only one of three options or none of them can be used in the same run.
  −
* --kinFile let RMW read in a kinship matrix from a file. The first row of the kinship file has to be the sample IDs included in the kinship file. If a sample of interest is not included in the kinship file, fatal error will occur and the program will be terminated. A sample of interest is a sample that is phenotyped and has all covariates measured when --makeResiduals is specified.
  −
* --kinSave allows you to save the kinship matrix.
  −
 
  −
==== Kinship Options ====
  −
* --kinMiss and --kinMaf should be used with --kinGeno together.
  −
* --kinMiss specifies the maximum genotype missing rate when calculating kinship from genotypes. The default is 0.05.
  −
* --kinMaf specifies the minimum minor allele frequency used when calculating kinship from genotypes. The default is 0.05.
  −
 
  −
==== Chromosome X ====
  −
* --xLabel should have a value of a string which specifies how variants on chromosome X are coded. The default is "X".
  −
* --xStart and --xEnd specifies the start and end of non-pseudo-autosomal regions on chromosome X. These options should be specified when --vcX is used.
  −
* The default for --xStart is 2699520 and default for --xEnd is 154931044, according to NCBI genome build 37.
  −
 
  −
Please refer to the following for the analysis of X-linked variants [[RAREMETALWORKER_X|'''ANALYZING CHROMOSOME X''']].
  −
 
  −
{{PhoneHomeParameters|hdr=====|bullet=1}}
 
Abought
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