Difference between revisions of "RAREMETAL Command Reference"

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[[Category:RAREMETAL]]
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==Useful Pages==
 +
* The [[RAREMETAL| Home Page]]
  
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=== Overview of options ===
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* The [[RAREMETAL_Documentation|RAREMETAL Documentation]]
 +
 
 +
* The [[Tutorial:_RAREMETAL|RAREMETAL Tutorial]]
 +
 
 +
* The [[RAREMETAL FAQ]]
 +
 
 +
* The [[RAREMETALWORKER | RAREMETALWORKER documentation]]
 +
 
 +
==Command References==
 +
=== Overview of Options ===
 
  Options:
 
  Options:
 
       List of Studies : --studyName []
 
       List of Studies : --studyName []
 
       Grouping Methods : --groupFile [], --annotatedVcf [], --annotation [],
 
       Grouping Methods : --groupFile [], --annotatedVcf [], --annotation [],
 
                         --writeVcf
 
                         --writeVcf
−
             QC Options : --hwe [0.00], --callRate [0.00]
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             QC Options : --hwe [1.0e-05], --callRate [0.95]
 
   Association Methods : --burden, --MB, --SKAT, --VT, --condition []
 
   Association Methods : --burden, --MB, --SKAT, --VT, --condition []
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         Other Options : --tabix, --correctGC, --prefix [], --maf [0.05],
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         Other Options : --labelHits, --correctGC, --prefix [],
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                        --mapFile [../src/refFlat_hg19.txt], --maf [0.05],
 
                         --longOutput, --tabulateHits, --hitsCutoff [1.0e-06]
 
                         --longOutput, --tabulateHits, --hitsCutoff [1.0e-06]
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                        --altMAF
  
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=== Describing Input Files ===
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=== Describing Studies ===
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   SEPARATOR        [WHITESPACE|COMMA|BOTH|TAB] (default = WHITESPACE)
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   --studyName [your.list.of.studies.file]
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  COLUMNCOUNTING  [STRICT|LENIENT]            (default = 'STRICT')
 
−
  MARKERLABEL      [LABEL]                    (default = 'MARKER')
 
−
  ALLELELABELS    [LABEL1 LABEL2]            (default = 'ALLELE1','ALLELE2')
 
−
  EFFECTLABEL      [LABEL|log(LABEL)]          (default = 'EFFECT')
 
−
  FLIP
 
−
 
 
−
Additional details on the [[METAL COLUMNCOUNTING|COLUMNCOUNTING]] and [[METAL EFFECTLABEL|EFFECTLABEL]] options are available.
 
−
 
 
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=== Filtering Input Files ===
 
−
  ADDFILTER        [LABEL CONDITION VALUE]    (example = ADDFILTER N > 10)
 
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                    (available conditions are <, >, <=, >=, =, !=, IN)
 
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  REMOVEFILTERS
 
−
 
 
−
Additional details on these options are [[METAL ADDFILTER|available]].
 
−
 
 
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=== Sample Size Weighted Meta-analysis ===
 
−
  WEIGHTLABEL      [LABEL]                    (default = 'N')
 
−
  PVALUELABEL      [LABEL]                    (default = 'PVALUE')
 
−
  DEFAULTWEIGHT    [NUMBER]                    (default = 1.0)
 
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  MINWEIGHT        [NUMBER]                    (default = 1.0)
 
−
 
 
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=== Inverse Variance Weighted Meta-analysis ===
 
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  STDERRLABEL      [LABEL]                    (default = 'STDERR')
 
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  SCHEME          [SAMPLESIZE|STDERR]        (default = SAMPLESIZE)
 
−
 
 
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=== Tracking of Allele Frequencies ===
 
−
  AVERAGEFREQ      [ON|OFF]                    (default = OFF)
 
−
  MINMAXFREQ      [ON|OFF]                    (default = OFF)
 
−
  FREQLABEL        [LABEL]                    (default = 'FREQ')
 
−
 
 
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=== User Defined Variables ===
 
−
  CUSTOMVARIABLE  [VARNAME]
 
−
  LABEL            [VARNAME] AS [HEADER]
 
  
−
Additional details on these options are [[METAL CUSTOMVARIABLE|available]].
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Additional details on this option is [[Rare-Metal#List_of_Studies_2|available]].
  
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=== Explicit Strand Information ===
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=== Methods to Group Rare Variants ===
−
  USESTRAND        [ON|OFF]                    (default = OFF)
 
−
  STRANDLABEL      [LABEL]                    (default = 'STRAND')
 
  
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=== Genomic Control Correction of Input Statistics ===
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--groupFile      [your.groups.file]
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  GENOMICCONTROL   [ON|OFF|VALUE|LIST snps.txt](default = OFF)
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--annotatedVcf   [your.annotated.vcf]
 +
--annotation    [nonsyn/stop/splice]
 +
--writeVcf      [ON|OFF]
  
−
Additional details on this option are [[METAL GENOMICCONTROL|available]].
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Additional details on [[Rare-Metal#Grouping_from_a_Group_File|groupFile]], [[Rare-Metal#Grouping_from_an_Annotated_VCF_File|annotatedVcf, annotation]] and [[Rare-Metal#Generate_a_VCF_File_to_Annotate_Outside_of_Rare_Metal|writeVcf]] options are available.
  
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=== General Analysis Control ===
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=== QC Options ===
−
   PROCESSFILE      [FILENAME]
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   --hwe            [hwe.pvalue.cutoff]                     (default = 1e-05)
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  OUTFILE          [PREFIX SUFFIX]            (default = 'METAANALYSIS','.TBL')
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   --callRate     [variant.call.rate.cutoff]               (default = 0.95)
−
   MAXWARNINGS     [NUMBER]                   (default = 20)
 
−
  VERBOSE          [ON|OFF]                    (default = 'OFF')
 
−
  LOGPVALUE        [ON|OFF]                    (default = 'OFF')
 
−
  ANALYZE          [HETEROGENEITY]
 
−
  CLEAR
 
  
−
Additional details on the [[METAL LOGPVALUE|LogPValue]] and [[METAL VERBOSE|Verbose]] commands are available.
+
Additional details on these options are [[Rare-Metal#QC_Options|available]].
  
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=== Script Control ===
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=== Association Methods for Meta-analysis ===
 +
  --useExact  optimized method for unbalanced studies with unrelated samples,
 +
                            described [[RAREMETAL METHOD#SINGLE_VARIANT_SCORE_TEST]].
 +
  --burden      burden test with equal weight       
 +
  --MAB        burden test with MAF as weight
 +
  --MB          burden test with sqrt(maf(1-maf)) as weight
 +
  --BBeta    beta distribution as weight
 +
  --VT          variant threshold test
 +
  --SKAT        standard SKAT test
 +
  --condition  [your.list.of variants.to.be.conditioned.upon]
 +
Additional details for these options are [[Rare-Metal#Association_Methods|available]].
  
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   SOURCE            [FILENAME]
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=== Other Options for Performance and Amenities ===
 +
  --labelHits   [ON|OFF]
 +
  --correctGC    [ON|OFF]
 +
  --prefix      [your.prefix]
 +
  --maf          [your.maf.threshold.for.gene-level.tests]    (default = 0.05)
 +
  --longOutput  [ON|OFF]
 +
  --tabulateHits [ON|OFF]
 +
  --hitsCutoff  [your.cutoff.for.hits]                      (default = 1e-06)
 +
  --altMAF      [if specified, studies that do not contain the variant will be excluded.]
  
−
Additional details on this command are [[METAL SOURCE|available]].
+
Additional details for these options are [[Rare-Metal#Other_Options|available]].

Latest revision as of 17:53, 16 March 2018

Useful Pages

Command References

Overview of Options

Options:
      List of Studies : --studyName []
     Grouping Methods : --groupFile [], --annotatedVcf [], --annotation [],
                        --writeVcf
           QC Options : --hwe [1.0e-05], --callRate [0.95]
  Association Methods : --burden, --MB, --SKAT, --VT, --condition []
        Other Options : --labelHits, --correctGC, --prefix [],
                        --mapFile [../src/refFlat_hg19.txt], --maf [0.05],
                        --longOutput, --tabulateHits, --hitsCutoff [1.0e-06]
                        --altMAF

Describing Studies

  --studyName [your.list.of.studies.file]

Additional details on this option is available.

Methods to Group Rare Variants

--groupFile      [your.groups.file]
--annotatedVcf   [your.annotated.vcf]
--annotation     [nonsyn/stop/splice]
--writeVcf       [ON|OFF]

Additional details on groupFile, annotatedVcf, annotation and writeVcf options are available.

QC Options

  --hwe            [hwe.pvalue.cutoff]                     (default = 1e-05)
  --callRate      [variant.call.rate.cutoff]               (default = 0.95)

Additional details on these options are available.

Association Methods for Meta-analysis

  --useExact   optimized method for unbalanced studies with unrelated samples,
                           described RAREMETAL METHOD#SINGLE_VARIANT_SCORE_TEST.
  --burden      burden test with equal weight        
  --MAB         burden test with MAF as weight
  --MB          burden test with sqrt(maf(1-maf)) as weight
  --BBeta     beta distribution as weight
  --VT           variant threshold test
  --SKAT         standard SKAT test
  --condition   [your.list.of variants.to.be.conditioned.upon]

Additional details for these options are available.

Other Options for Performance and Amenities

 --labelHits    [ON|OFF]
 --correctGC    [ON|OFF]
 --prefix       [your.prefix]
 --maf          [your.maf.threshold.for.gene-level.tests]    (default = 0.05)
 --longOutput   [ON|OFF]
 --tabulateHits [ON|OFF]
 --hitsCutoff   [your.cutoff.for.hits]                       (default = 1e-06)
 --altMAF       [if specified, studies that do not contain the variant will be excluded.]

Additional details for these options are available.

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