Changes

From Genome Analysis Wiki
Jump to navigationJump to search

RAREMETAL Command Reference (view source)

Revision as of 17:53, 16 March 2018

185 bytes added ,  17:53, 16 March 2018
no edit summary
Line 1: Line 1:  +
[[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]].
 
Abought
32

edits

Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/7768...15013"

Navigation menu