Difference between revisions of "RAREMETAL Command Reference"
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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 [ | + | 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 : -- | + | 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 | + | --useExact optimized method for unbalanced studies with unrelated samples, |
− | --MB | + | described [[RAREMETAL METHOD#SINGLE_VARIANT_SCORE_TEST]]. |
− | --VT | + | --burden burden test with equal weight |
− | --SKAT | + | --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] | --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]]. |
Latest revision as of 17:53, 16 March 2018
Useful Pages
- The Home Page
- The RAREMETAL FAQ
Command References
Overview of Options
Options: List of Studies : --studyName [] Grouping Methods : --groupFile [], --annotatedVcf [], --annotation [], --writeVcf QC Options : --hwe [1.0e-05], --callRate [0.95] Association Methods : --burden, --MB, --SKAT, --VT, --condition [] Other Options : --labelHits, --correctGC, --prefix [], --mapFile [../src/refFlat_hg19.txt], --maf [0.05], --longOutput, --tabulateHits, --hitsCutoff [1.0e-06] --altMAF
Describing Studies
--studyName [your.list.of.studies.file]
Additional details on this option is available.
Methods to Group Rare Variants
--groupFile [your.groups.file] --annotatedVcf [your.annotated.vcf] --annotation [nonsyn/stop/splice] --writeVcf [ON|OFF]
Additional details on groupFile, annotatedVcf, annotation and writeVcf options are available.
QC Options
--hwe [hwe.pvalue.cutoff] (default = 1e-05) --callRate [variant.call.rate.cutoff] (default = 0.95)
Additional details on these options are available.
Association Methods for Meta-analysis
--useExact optimized method for unbalanced studies with unrelated samples, described RAREMETAL METHOD#SINGLE_VARIANT_SCORE_TEST. --burden burden test with equal weight --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]
Additional details for these options are available.
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 for these options are available.