From Genome Analysis Wiki
Jump to navigationJump to search
473 bytes added
, 17:53, 16 March 2018
Line 1: |
Line 1: |
| + | [[Category:RAREMETAL]] |
| ==Useful Pages== | | ==Useful Pages== |
− | * The [[RAREMETAL Command Reference]] | + | * The [[RAREMETAL| Home Page]] |
| | | |
| * The [[RAREMETAL_Documentation|RAREMETAL Documentation]] | | * The [[RAREMETAL_Documentation|RAREMETAL Documentation]] |
Line 10: |
Line 11: |
| * The [[RAREMETALWORKER | RAREMETALWORKER documentation]] | | * The [[RAREMETALWORKER | RAREMETALWORKER documentation]] |
| | | |
− | ==Commands== | + | ==Command References== |
| === Overview of Options === | | === Overview of Options === |
| Options: | | Options: |
Line 21: |
Line 22: |
| --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 === |
Line 43: |
Line 45: |
| | | |
| === 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]]. |
Line 58: |
Line 64: |
| --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]]. |