RAREMETAL Command Reference
From Genome Analysis Wiki
Revision as of 14:41, 7 August 2013 by Shuang Feng (talk | contribs) (→Other Options for Performance and Amenities)
Overview of Options
Options: List of Studies : --studyName [] Grouping Methods : --groupFile [], --annotatedVcf [], --annotation [], --writeVcf QC Options : --hwe [1e-05], --callRate [0.95] Association Methods : --burden, --MB, --SKAT, --VT, --condition [] Other Options : --tabix, --correctGC, --prefix [], --maf [0.05], --longOutput, --tabulateHits, --hitsCutoff [1.0e-06]
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
--burden [ON|OFF] --MB [ON|OFF] --VT [ON|OFF] --SKAT [ON|OFF] --condition [your.list.of variants.to.be.conditioned.upon]
Additional details for these options are available.
Other Options for Performance and Amenities
----tabix [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)
User Defined Variables
CUSTOMVARIABLE [VARNAME] LABEL [VARNAME] AS [HEADER]
Additional details on these options are available.
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)
Additional details on this option are available.
General Analysis Control
PROCESSFILE [FILENAME] OUTFILE [PREFIX SUFFIX] (default = 'METAANALYSIS','.TBL') MAXWARNINGS [NUMBER] (default = 20) VERBOSE [ON|OFF] (default = 'OFF') LOGPVALUE [ON|OFF] (default = 'OFF') ANALYZE [HETEROGENEITY] CLEAR
Additional details on the LogPValue and Verbose commands are available.
Script Control
SOURCE [FILENAME]
Additional details on this command are available.