RAREMETAL Command Reference
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Revision as of 16:08, 27 November 2016 by Saichen (talk | contribs) (→Association Methods for Meta-analysis)
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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
--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.
