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RAREMETAL Command Reference

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==Useful Pages==
* The [[RAREMETAL| Home Page]]
* The [[RAREMETAL_Documentation|RAREMETAL Documentation]] * The [[Tutorial:_RAREMETAL|RAREMETAL Tutorial]]  * The [[RAREMETAL FAQ]] * The [[RAREMETALWORKER | RAREMETALWORKER documentation]] ==Command References===== Overview of options Options ===
List of Studies : --studyName []
Grouping Methods : --groupFile [], --annotatedVcf [], --annotation [],
QC Options : --hwe [1e1.0e-05], --callRate [0.95]
Association Methods : --burden, --MB, --SKAT, --VT, --condition []
Other Options : --tabixlabelHits, --correctGC, --prefix [], --mapFile [../src/refFlat_hg19.txt], --maf [0.05],
--longOutput, --tabulateHits, --hitsCutoff [1.0e-06]
=== Describing Input Files Studies === SEPARATOR --studyName [WHITESPACE|COMMA|BOTH|TAB] (default = WHITESPACE) COLUMNCOUNTING [STRICT|LENIENT] (default = 'STRICT') MARKERLABEL [LABEL] (default = 'MARKER') ALLELELABELS [LABEL1 LABEL2] (default = 'ALLELE1','ALLELE2') EFFECTLABEL [LABEL|log(LABEL)] (default = 'EFFECT') FLIP Additional details on the [[METAL COLUMNCOUNTING|COLUMNCOUNTING]] and [[METAL EFFECTLABEL|EFFECTLABEL]] options are availableyour=== Filtering Input Files === ADDFILTER [LABEL CONDITION VALUE] (example = ADDFILTER N > 10) (available conditions are <, >, <=, >=, =, !=, IN) REMOVEFILTERS Additional details on these options are [[METAL ADDFILTER|available]]list=== Sample Size Weighted Meta-analysis === WEIGHTLABEL [LABEL] (default = 'N') PVALUELABEL [LABEL] (default = 'PVALUE') DEFAULTWEIGHT [NUMBER] (default = 1of.0) MINWEIGHT [NUMBER] (default = 1studies.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 [HEADERfile]
Additional details on these options are this option is [[METAL CUSTOMVARIABLERare-Metal#List_of_Studies_2|available]].
=== Explicit Strand Information Methods to Group Rare Variants === USESTRAND [ON|OFF] (default = OFF) STRANDLABEL [LABEL] (default = 'STRAND')
=== Genomic Control Correction of Input Statistics === --groupFile [your.groups.file] GENOMICCONTROL --annotatedVcf [your.annotated.vcf] --annotation [nonsyn/stop/splice] --writeVcf [ON|OFF|VALUE|LIST snps.txt](default = OFF)
Additional details on this option are [[METAL GENOMICCONTROLRare-Metal#Grouping_from_a_Group_File|groupFile]], [[Rare-Metal#Grouping_from_an_Annotated_VCF_File|annotatedVcf, annotation]] and [[Rare-Metal#Generate_a_VCF_File_to_Annotate_Outside_of_Rare_Metal|availablewriteVcf]]options are available.
=== General Analysis Control QC Options === PROCESSFILE --hwe [FILENAMEhwe.pvalue.cutoff] OUTFILE [PREFIX SUFFIX] (default = 'METAANALYSIS','.TBL'1e-05) MAXWARNINGS --callRate [] (default = 20) VERBOSE [ON|OFF] (default = 'OFF'0.95) LOGPVALUE [ON|OFF] (default = 'OFF') ANALYZE [HETEROGENEITY] CLEAR
Additional details on the these options are [[METAL LOGPVALUERare-Metal#QC_Options|LogPValueavailable]] and [[METAL VERBOSE|Verbose]] commands are available.
=== Script Control 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 --BBeta beta distribution as weight --VT variant threshold test --SKAT standard SKAT test --condition [your.list.of]Additional details for these options are [[Rare-Metal#Association_Methods|available]].
=== Other Options for Performance and Amenities === --labelHits SOURCE [FILENAMEON|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 on this command for these options are [[METAL SOURCERare-Metal#Other_Options|available]].