Difference between revisions of "RAREMETAL Command Reference"

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(Methods to Group Rare Variants)
(Sample Size Weighted Meta-analysis)
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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.
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.
=== Sample Size Weighted Meta-analysis ===
=== QC Options ===
   WEIGHTLABEL      [LABEL]                    (default = 'N')
   --hwe            [hwe.pvalue.cutoff]                    (default = 1e-05)
   PVALUELABEL     [LABEL]                    (default = 'PVALUE')
   --callRate     [variant.call.rate.cutoff]               (default = 0.95)
  DEFAULTWEIGHT    [NUMBER]                   (default = 1.0)
  MINWEIGHT        [NUMBER]                    (default = 1.0)
=== Inverse Variance Weighted Meta-analysis ===
=== Inverse Variance Weighted Meta-analysis ===

Revision as of 13:29, 7 August 2013

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)

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

  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.