RAREMETAL Command Reference: Difference between revisions

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[[Category:RAREMETAL]]
==Useful Pages==
* The [[RAREMETAL| Home Page]]


=== Describing Input Files ===
* The [[RAREMETAL_Documentation|RAREMETAL Documentation]]
  SEPARATOR        [WHITESPACE|COMMA|BOTH|TAB] (default = WHITESPACE)
  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.
* The [[Tutorial:_RAREMETAL|RAREMETAL Tutorial]]  


=== Filtering Input Files ===
* The [[RAREMETAL FAQ]]
  ADDFILTER        [LABEL CONDITION VALUE]     (example = ADDFILTER N > 10)
                    (available conditions are <, >, <=, >=, =, !=, IN)
  REMOVEFILTERS


Additional details on these options are [[METAL ADDFILTER|available]].
* The [[RAREMETALWORKER | RAREMETALWORKER documentation]]


=== Sample Size Weighted Meta-analysis ===
==Command References==
  WEIGHTLABEL      [LABEL]                     (default = 'N')
=== Overview of Options ===
  PVALUELABEL      [LABEL]                     (default = 'PVALUE')
Options:
  DEFAULTWEIGHT    [NUMBER]                    (default = 1.0)
      List of Studies : --studyName []
   MINWEIGHT        [NUMBER]                   (default = 1.0)
      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


=== Inverse Variance Weighted Meta-analysis ===
=== Describing Studies ===
   STDERRLABEL      [LABEL]                     (default = 'STDERR')
   --studyName [your.list.of.studies.file]
  SCHEME          [SAMPLESIZE|STDERR]        (default = SAMPLESIZE)


=== Tracking of Allele Frequencies ===
Additional details on this option is [[Rare-Metal#List_of_Studies_2|available]].
  AVERAGEFREQ      [ON|OFF]                    (default = OFF)
  MINMAXFREQ      [ON|OFF]                   (default = OFF)
  FREQLABEL        [LABEL]                     (default = 'FREQ')


=== User Defined Variables ===
=== Methods to Group Rare Variants ===
  CUSTOMVARIABLE  [VARNAME]
  LABEL            [VARNAME] AS [HEADER]


Additional details on these options are [[METAL CUSTOMVARIABLE|available]].
--groupFile      [your.groups.file]
--annotatedVcf  [your.annotated.vcf]
--annotation    [nonsyn/stop/splice]
--writeVcf      [ON|OFF]


=== Explicit Strand Information ===
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.
  USESTRAND        [ON|OFF]                   (default = OFF)
  STRANDLABEL      [LABEL]                     (default = 'STRAND')


=== Genomic Control Correction of Input Statistics ===
=== QC Options ===
   GENOMICCONTROL  [ON|OFF|VALUE|LIST snps.txt](default = OFF)
   --hwe            [hwe.pvalue.cutoff]                    (default = 1e-05)
  --callRate      [variant.call.rate.cutoff]               (default = 0.95)


Additional details on this option are [[METAL GENOMICCONTROL|available]].
Additional details on these options are [[Rare-Metal#QC_Options|available]].


=== General Analysis Control ===
=== Association Methods for Meta-analysis ===
   PROCESSFILE      [FILENAME]
   --useExact  optimized method for unbalanced studies with unrelated samples,
  OUTFILE          [PREFIX SUFFIX]             (default = 'METAANALYSIS','.TBL')
                            described [[RAREMETAL METHOD#SINGLE_VARIANT_SCORE_TEST]].
   MAXWARNINGS     [NUMBER]                    (default = 20)
   --burden     burden test with equal weight       
   VERBOSE         [ON|OFF]                    (default = 'OFF')
  --MAB        burden test with MAF as weight
   LOGPVALUE        [ON|OFF]                   (default = 'OFF')
   --MB         burden test with sqrt(maf(1-maf)) as weight
  ANALYZE          [HETEROGENEITY]
   --BBeta    beta distribution as weight
  CLEAR
  --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]].


Additional details on the [[METAL LOGPVALUE|LogPValue]] and [[METAL VERBOSE|Verbose]] commands 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.]


=== Script Control ===
Additional details for these options are [[Rare-Metal#Other_Options|available]].
 
  SOURCE            [FILENAME]
 
Additional details on this command are [[METAL SOURCE|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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