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RAREMETAL Command Reference

185 bytes added, 17:53, 16 March 2018
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[[Category:RAREMETAL]]
==Useful Pages==
* The [[RAREMETAL| Home Page]]
=== Describing Input Files === SEPARATOR * The [WHITESPACE|COMMA|BOTH|TAB] (default = WHITESPACE) COLUMNCOUNTING [STRICTRAREMETAL_Documentation|LENIENT] (default = 'STRICT') MARKERLABEL [LABELRAREMETAL Documentation] (default = 'MARKER') ALLELELABELS [LABEL1 LABEL2] (default = 'ALLELE1','ALLELE2') EFFECTLABEL [LABEL|log(LABEL)] (default = 'EFFECT') FLIP
Additional details on the * The [[METAL COLUMNCOUNTINGTutorial:_RAREMETAL|COLUMNCOUNTINGRAREMETAL Tutorial]] and [[METAL EFFECTLABEL|EFFECTLABEL]] options are available.
=== Filtering Input Files === ADDFILTER * The [LABEL CONDITION VALUE[RAREMETAL FAQ]] (example = ADDFILTER N > 10) (available conditions are <, >, <=, >=, =, !=, IN) REMOVEFILTERS
Additional details on these options are * The [[METAL ADDFILTERRAREMETALWORKER |availableRAREMETALWORKER documentation]].
==Command References= Sample Size Weighted Meta-analysis ==== Overview of Options === WEIGHTLABEL Options: List of Studies : --studyName [LABEL] (default = 'N') PVALUELABEL Grouping Methods : --groupFile [], --annotatedVcf [], --annotation [LABEL] (default = 'PVALUE'), --writeVcf DEFAULTWEIGHT QC Options : --hwe [NUMBER] (default = 1.0e-05], --callRate [0).95] MINWEIGHT Association Methods : --burden, --MB, --SKAT, --VT, --condition [] Other Options : --labelHits, --correctGC, --prefix [], --mapFile [../src/refFlat_hg19.txt], --maf [NUMBER0.05] (default = , --longOutput, --tabulateHits, --hitsCutoff [1.0)0e-06] --altMAF
=== Inverse Variance Weighted Meta-analysis Describing Studies === STDERRLABEL --studyName [LABELyour.list.of.studies.file] (default = 'STDERR') SCHEME [SAMPLESIZE|STDERR] (default = SAMPLESIZE)
=== Tracking of Allele Frequencies === AVERAGEFREQ Additional details on this option is [ON|OFF] (default = OFF) MINMAXFREQ [ONRare-Metal#List_of_Studies_2|OFFavailable] (default = OFF) FREQLABEL [LABEL] (default = 'FREQ').
=== User Defined Variables Methods to Group Rare Variants === CUSTOMVARIABLE [VARNAME] LABEL [VARNAME] AS [HEADER]
Additional details on these options are --groupFile [your.groups.file] --annotatedVcf [METAL CUSTOMVARIABLEyour.annotated.vcf] --annotation [nonsyn/stop/splice] --writeVcf [ON|availableOFF]].
=== Explicit Strand Information === USESTRAND Additional details on [ON[Rare-Metal#Grouping_from_a_Group_File|groupFile]], [[Rare-Metal#Grouping_from_an_Annotated_VCF_File|OFFannotatedVcf, annotation] (default = OFF) STRANDLABEL ] and [LABEL[Rare-Metal#Generate_a_VCF_File_to_Annotate_Outside_of_Rare_Metal|writeVcf]] (default = 'STRAND')options are available.
=== Genomic Control Correction of Input Statistics QC Options === GENOMICCONTROL --hwe [ON|OFF|VALUE|LIST snpshwe.txtpvalue.cutoff] (default = 1e-05) --callRate [variant.call.rate.cutoff] (default = OFF0.95)
Additional details on this option these options are [[METAL GENOMICCONTROLRare-Metal#QC_Options|available]].
=== General Analysis Control Association Methods for Meta-analysis === PROCESSFILE --useExact optimized method for unbalanced studies with unrelated samples, described [[FILENAMERAREMETAL METHOD#SINGLE_VARIANT_SCORE_TEST] OUTFILE [PREFIX SUFFIX] (default = 'METAANALYSIS','.TBL') MAXWARNINGS --burden [NUMBER] (default = 20)burden test with equal weight --MAB burden test with MAF as weight VERBOSE --MB [ON|OFF] burden test with sqrt(maf(default = 'OFF'1-maf))as weight LOGPVALUE --BBeta beta distribution as weight --VT variant threshold test --SKAT standard SKAT test --condition [ON|OFFyour.list.of variants.to.be.conditioned.upon] (default = 'OFF') ANALYZE Additional details for these options are [[HETEROGENEITYRare-Metal#Association_Methods|available]] CLEAR.
Additional details on the === Other Options for Performance and Amenities === --labelHits [ON|OFF] --correctGC [METAL LOGPVALUEON|LogPValueOFF] --prefix [your.prefix] --maf [your.maf.threshold.for.gene-level.tests] and (default = 0.05) --longOutput [ON|OFF] --tabulateHits [METAL VERBOSEON|VerboseOFF] --hitsCutoff [your.cutoff.for.hits] commands are available (default = 1e-06) --altMAF [if specified, studies that do not contain the variant will be excluded.]
=== Script Control ===  SOURCE [FILENAME] Additional details on this command for these options are [[METAL SOURCERare-Metal#Other_Options|available]].
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