From Genome Analysis Wiki
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13:42, 7 August 2013
=== Overview of Options ===
Options:
--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 [[METAL CUSTOMVARIABLE|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 [[METAL GENOMICCONTROL|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 [[METAL LOGPVALUE|LogPValue]] and [[METAL VERBOSE|Verbose]] commands are available.
=== Script Control ===
SOURCE [FILENAME]
Additional details on this command are [[METAL SOURCE|available]].
