Difference between revisions of "RAREMETAL Command Reference"
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--studyName [your.list.of.studies] | --studyName [your.list.of.studies] | ||
| − | Additional details on the [[http://genome.sph.umich.edu/wiki/Rare-Metal#List_of_Studies_2 | + | Additional details on the [[http://genome.sph.umich.edu/wiki/Rare-Metal#List_of_Studies_2|--studyName]] option is available. |
=== Filtering Input Files === | === Filtering Input Files === | ||
Revision as of 13:13, 7 August 2013
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]
Additional details on the [[1]] option is available.
Filtering Input Files
ADDFILTER [LABEL CONDITION VALUE] (example = ADDFILTER N > 10)
(available conditions are <, >, <=, >=, =, !=, IN)
REMOVEFILTERS
Additional details on these options are available.
Sample Size Weighted Meta-analysis
WEIGHTLABEL [LABEL] (default = 'N') PVALUELABEL [LABEL] (default = 'PVALUE') DEFAULTWEIGHT [NUMBER] (default = 1.0) MINWEIGHT [NUMBER] (default = 1.0)
Inverse Variance Weighted Meta-analysis
STDERRLABEL [LABEL] (default = 'STDERR') SCHEME [SAMPLESIZE|STDERR] (default = SAMPLESIZE)
Tracking of Allele Frequencies
AVERAGEFREQ [ON|OFF] (default = OFF) MINMAXFREQ [ON|OFF] (default = OFF) FREQLABEL [LABEL] (default = 'FREQ')
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.
