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[[Category:RAREMETAL]]
==Useful Pages==
==Useful Pages==
* The [[RAREMETAL| Home Page]]
* The [[RAREMETAL| Home Page]]
--mapFile [../src/refFlat_hg19.txt], --maf [0.05],
--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]].
--tabulateHits [ON|OFF]
--tabulateHits [ON|OFF]
--hitsCutoff [your.cutoff.for.hits] (default = 1e-06)
--hitsCutoff [your.cutoff.for.hits] (default = 1e-06)
--altMAF [if specified, studies that do not contain the variant will be excluded.]
--altMAF [if specified, studies that do not contain the variant will be excluded.]
Additional details for these options are [[Rare-Metal#Other_Options|available]].
Additional details for these options are [[Rare-Metal#Other_Options|available]].
