View source for RAREMETAL Command Reference

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

* The [[RAREMETAL_Documentation|RAREMETAL Documentation]]

* The [[Tutorial:_RAREMETAL|RAREMETAL Tutorial]] 

* The [[RAREMETAL FAQ]]

* The [[RAREMETALWORKER | RAREMETALWORKER documentation]]

==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]
                         --dosage, --altMAF

=== Describing Studies ===
   --studyName [your.list.of.studies.file]

Additional details on this option is [[Rare-Metal#List_of_Studies_2|available]].

=== Methods to Group Rare Variants ===

 --groupFile      [your.groups.file]
 --annotatedVcf   [your.annotated.vcf]
 --annotation     [nonsyn/stop/splice]
 --writeVcf       [ON|OFF]

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.

=== QC Options ===
   --hwe            [hwe.pvalue.cutoff]                     (default = 1e-05)
   --callRate      [variant.call.rate.cutoff]               (default = 0.95)

Additional details on these options are [[Rare-Metal#QC_Options|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 [[Rare-Metal#Association_Methods|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 [[Rare-Metal#Other_Options|available]].