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[[Category:RAREMETAL]]
==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 ===
=== Overview of Options ===
Options:
Options:
Grouping Methods : --groupFile [], --annotatedVcf [], --annotation [],
Grouping Methods : --groupFile [], --annotatedVcf [], --annotation [],
--writeVcf
--writeVcf
QC Options : --hwe [1e-05], --callRate [0.95]
QC Options : --hwe [1.0e-05], --callRate [0.95]
Association Methods : --burden, --MB, --SKAT, --VT, --condition []
Association Methods : --burden, --MB, --SKAT, --VT, --condition []
Other Options : --tabix, --correctGC, --prefix [], --maf [0.05],
Other Options : --labelHits, --correctGC, --prefix [],
--mapFile [../src/refFlat_hg19.txt], --maf [0.05],
--longOutput, --tabulateHits, --hitsCutoff [1.0e-06]
--longOutput, --tabulateHits, --hitsCutoff [1.0e-06]
--altMAF
=== Describing Studies ===
=== Describing Studies ===
=== Association Methods for Meta-analysis ===
=== Association Methods for Meta-analysis ===
--burden [ON|OFF]
--useExact optimized method for unbalanced studies with unrelated samples,
--MB [ON|OFF]
described [[RAREMETAL METHOD#SINGLE_VARIANT_SCORE_TEST]].
--VT [ON|OFF]
--burden burden test with equal weight
--SKAT [ON|OFF]
--MAB burden test with MAF as weight
--MB burden test with sqrt(maf(1-maf)) as weight
--BBeta beta distribution as weight
--VT variant threshold test
--SKAT standard SKAT test
--condition [your.list.of variants.to.be.conditioned.upon]
--condition [your.list.of variants.to.be.conditioned.upon]
Additional details for these options are [[Rare-Metal#Association_Methods|available]].
Additional details for these options are [[Rare-Metal#Association_Methods|available]].
=== Tracking of Allele Frequencies ===
=== 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 on this command are [[METAL SOURCE|available]].
Additional details for these options are [[Rare-Metal#Other_Options|available]].
