RAREMETAL Command Reference

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Revision as of 14:41, 7 August 2013 by Shuang Feng (talk | contribs) (Other Options for Performance and Amenities)
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Overview of Options

      List of Studies : --studyName []
     Grouping Methods : --groupFile [], --annotatedVcf [], --annotation [],
           QC Options : --hwe [1e-05], --callRate [0.95]
  Association Methods : --burden, --MB, --SKAT, --VT, --condition []
        Other Options : --tabix, --correctGC, --prefix [], --maf [0.05],
                        --longOutput, --tabulateHits, --hitsCutoff [1.0e-06]

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

  --burden      [ON|OFF]                  
  --MB          [ON|OFF]       
  --VT          [ON|OFF]
  --SKAT        [ON|OFF]
  --condition   [your.list.of variants.to.be.conditioned.upon]

Additional details for these options are available.

Other Options for Performance and Amenities

 ----tabix      [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)

User Defined Variables

  LABEL            [VARNAME] AS [HEADER]

Additional details on these options are available.

Explicit Strand Information

  USESTRAND        [ON|OFF]                    (default = OFF)
  STRANDLABEL      [LABEL]                     (default = 'STRAND')

Genomic Control Correction of Input Statistics

  GENOMICCONTROL   [ON|OFF|VALUE|LIST snps.txt](default = OFF)

Additional details on this option are available.

General Analysis Control

  OUTFILE          [PREFIX SUFFIX]             (default = 'METAANALYSIS','.TBL')
  MAXWARNINGS      [NUMBER]                    (default = 20)
  VERBOSE          [ON|OFF]                    (default = 'OFF')
  LOGPVALUE        [ON|OFF]                    (default = 'OFF')

Additional details on the LogPValue and Verbose commands are available.

Script Control

  SOURCE            [FILENAME]

Additional details on this command are available.