RAREMETAL Command Reference: Difference between revisions
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==Useful Pages== | |||
* The [[RAREMETAL Command Reference]] | |||
* The [[RAREMETAL_Documentation|RAREMETAL Documentation]] | |||
* The [[Tutorial:_RAREMETAL|RAREMETAL Tutorial]] | |||
* The [[RAREMETAL FAQ]] | |||
* The [[RAREMETALWORKER | RAREMETALWORKER documentation]] | |||
=== Overview of Options === | === Overview of Options === | ||
Options: | Options: | ||
Revision as of 13:22, 26 August 2013
Useful Pages
- The RAREMETAL FAQ
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]
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
--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)
Additional details for these options are available.
