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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: |
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| 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 === |
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| | | |
| === 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]]. |
| | | |
| === Other Options for Performance and Amenities === | | === Other Options for Performance and Amenities === |
− | --tabix [ON|OFF] | + | --labelHits [ON|OFF] |
| --correctGC [ON|OFF] | | --correctGC [ON|OFF] |
| --prefix [your.prefix] | | --prefix [your.prefix] |
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| --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.] |
| | | |
| Additional details for these options are [[Rare-Metal#Other_Options|available]]. | | Additional details for these options are [[Rare-Metal#Other_Options|available]]. |