RAREMETAL Command Reference

Overview of Options

Options:
      List of Studies : --studyName []
     Grouping Methods : --groupFile [], --annotatedVcf [], --annotation [],
                        --writeVcf
           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 Input Files

  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 COLUMNCOUNTING and EFFECTLABEL options are available.

Filtering Input Files

  ADDFILTER        [LABEL CONDITION VALUE]     (example = ADDFILTER N > 10)
                   (available conditions are <, >, <=, >=, =, !=, IN)
  REMOVEFILTERS

Additional details on these options are available.

Sample Size Weighted Meta-analysis

  WEIGHTLABEL      [LABEL]                     (default = 'N')
  PVALUELABEL      [LABEL]                     (default = 'PVALUE')
  DEFAULTWEIGHT    [NUMBER]                    (default = 1.0)
  MINWEIGHT        [NUMBER]                    (default = 1.0)

Inverse Variance Weighted Meta-analysis

  STDERRLABEL      [LABEL]                     (default = 'STDERR')
  SCHEME           [SAMPLESIZE|STDERR]         (default = SAMPLESIZE)

Tracking of Allele Frequencies

  AVERAGEFREQ      [ON|OFF]                    (default = OFF)
  MINMAXFREQ       [ON|OFF]                    (default = OFF)
  FREQLABEL        [LABEL]                     (default = 'FREQ')

User Defined Variables

  CUSTOMVARIABLE   [VARNAME]
  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

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

Additional details on the LogPValue and Verbose commands are available.

Script Control

  SOURCE            [FILENAME]

Additional details on this command are available.