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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 === |
− | -- | + | --labelHits [ON|OFF] |
− | | + | --correctGC [ON|OFF] |
− | === User Defined Variables ===
| + | --prefix [your.prefix] |
− | CUSTOMVARIABLE [VARNAME] | + | --maf [your.maf.threshold.for.gene-level.tests] (default = 0.05) |
− | LABEL [VARNAME] AS [HEADER]
| + | --longOutput [ON|OFF] |
− | | + | --tabulateHits [ON|OFF] |
− | Additional details on these options are [[METAL CUSTOMVARIABLE|available]].
| + | --hitsCutoff [your.cutoff.for.hits] (default = 1e-06) |
− | | + | --altMAF [if specified, studies that do not contain the variant will be excluded.] |
− | === Explicit Strand Information ===
| |
− | USESTRAND [ON|OFF] (default = OFF) | |
− | STRANDLABEL [LABEL] (default = 'STRAND')
| |
− | | |
− | === Genomic Control Correction of Input Statistics ===
| |
− | GENOMICCONTROL [ON|OFF|VALUE|LIST snps.txt](default = OFF)
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− | | |
− | Additional details on this option are [[METAL GENOMICCONTROL|available]].
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− | | |
− | === General Analysis Control ===
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− | PROCESSFILE [FILENAME]
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− | OUTFILE [PREFIX SUFFIX] (default = 'METAANALYSIS','.TBL') | |
− | MAXWARNINGS [NUMBER] (default = 20)
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− | VERBOSE [ON|OFF] (default = 'OFF')
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− | LOGPVALUE [ON|OFF] (default = 'OFF')
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− | ANALYZE [HETEROGENEITY]
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− | CLEAR
| |
− | | |
− | Additional details on the [[METAL LOGPVALUE|LogPValue]] and [[METAL VERBOSE|Verbose]] commands are available.
| |
− | | |
− | === Script Control ===
| |
− | | |
− | SOURCE [FILENAME]
| |
| | | |
− | Additional details on this command are [[METAL SOURCE|available]]. | + | Additional details for these options are [[Rare-Metal#Other_Options|available]]. |