Difference between revisions of "RAREMETAL Command Reference"
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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 === |
| − | + | -- | |
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=== User Defined Variables === | === User Defined Variables === | ||
Revision as of 14:38, 7 August 2013
Contents
- 1 Overview of Options
- 2 Describing Studies
- 3 Methods to Group Rare Variants
- 4 QC Options
- 5 Association Methods for Meta-analysis
- 6 Other Options for Performance and Amenities
- 7 User Defined Variables
- 8 Explicit Strand Information
- 9 Genomic Control Correction of Input Statistics
- 10 General Analysis Control
- 11 Script Control
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
--
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.
