Difference between revisions of "RAREMETAL Command Reference"
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| + | [[Category:RAREMETAL]] | ||
==Useful Pages== | ==Useful Pages== | ||
| − | * The [[RAREMETAL | + | * The [[RAREMETAL| Home Page]] |
* The [[RAREMETAL_Documentation|RAREMETAL Documentation]] | * The [[RAREMETAL_Documentation|RAREMETAL Documentation]] | ||
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* The [[RAREMETALWORKER | RAREMETALWORKER documentation]] | * The [[RAREMETALWORKER | RAREMETALWORKER documentation]] | ||
| − | == | + | ==Command References== |
=== Overview of Options === | === Overview of Options === | ||
Options: | Options: | ||
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--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 | + | --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]]. | ||
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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.
