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| + | [[Category:RAREMETAL]] |
| + | ==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 === | | === Overview of Options === |
| Options: | | Options: |
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| Grouping Methods : --groupFile [], --annotatedVcf [], --annotation [], | | Grouping Methods : --groupFile [], --annotatedVcf [], --annotation [], |
| --writeVcf | | --writeVcf |
− | QC Options : --hwe [1e-05], --callRate [0.95] | + | QC Options : --hwe [1.0e-05], --callRate [0.95] |
| Association Methods : --burden, --MB, --SKAT, --VT, --condition [] | | Association Methods : --burden, --MB, --SKAT, --VT, --condition [] |
− | Other Options : --tabix, --correctGC, --prefix [], --maf [0.05], | + | Other Options : --labelHits, --correctGC, --prefix [], |
| + | --mapFile [../src/refFlat_hg19.txt], --maf [0.05], |
| --longOutput, --tabulateHits, --hitsCutoff [1.0e-06] | | --longOutput, --tabulateHits, --hitsCutoff [1.0e-06] |
| + | --altMAF |
| | | |
| === Describing Studies === | | === Describing Studies === |
− | --studyName [your.list.of.studies] | + | --studyName [your.list.of.studies.file] |
− | | |
− | Additional details on the [[http://genome.sph.umich.edu/wiki/Rare-Metal#List_of_Studies_2|--studyName]] option is available.
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− | | |
− | === Filtering Input Files ===
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− | ADDFILTER [LABEL CONDITION VALUE] (example = ADDFILTER N > 10)
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− | (available conditions are <, >, <=, >=, =, !=, IN)
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− | REMOVEFILTERS
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− | | |
− | Additional details on these options are [[METAL ADDFILTER|available]].
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− | | |
− | === Sample Size Weighted Meta-analysis ===
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− | WEIGHTLABEL [LABEL] (default = 'N')
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− | PVALUELABEL [LABEL] (default = 'PVALUE')
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− | DEFAULTWEIGHT [NUMBER] (default = 1.0)
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− | MINWEIGHT [NUMBER] (default = 1.0)
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− | | |
− | === Inverse Variance Weighted Meta-analysis ===
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− | STDERRLABEL [LABEL] (default = 'STDERR')
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− | SCHEME [SAMPLESIZE|STDERR] (default = SAMPLESIZE)
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− | | |
− | === Tracking of Allele Frequencies ===
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− | AVERAGEFREQ [ON|OFF] (default = OFF)
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− | MINMAXFREQ [ON|OFF] (default = OFF)
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− | FREQLABEL [LABEL] (default = 'FREQ')
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− | | |
− | === User Defined Variables ===
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− | CUSTOMVARIABLE [VARNAME]
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− | LABEL [VARNAME] AS [HEADER]
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| | | |
− | Additional details on these options are [[METAL CUSTOMVARIABLE|available]]. | + | Additional details on this option is [[Rare-Metal#List_of_Studies_2|available]]. |
| | | |
− | === Explicit Strand Information === | + | === Methods to Group Rare Variants === |
− | USESTRAND [ON|OFF] (default = OFF)
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− | STRANDLABEL [LABEL] (default = 'STRAND')
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| | | |
− | === Genomic Control Correction of Input Statistics ===
| + | --groupFile [your.groups.file] |
− | GENOMICCONTROL [ON|OFF|VALUE|LIST snps.txt](default = OFF)
| + | --annotatedVcf [your.annotated.vcf] |
| + | --annotation [nonsyn/stop/splice] |
| + | --writeVcf [ON|OFF] |
| | | |
− | Additional details on this option are [[METAL GENOMICCONTROL|available]]. | + | Additional details on [[Rare-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|writeVcf]] options are available. |
| | | |
− | === General Analysis Control === | + | === QC Options === |
− | PROCESSFILE [FILENAME] | + | --hwe [hwe.pvalue.cutoff] (default = 1e-05) |
− | OUTFILE [PREFIX SUFFIX] (default = 'METAANALYSIS','.TBL')
| + | --callRate [variant.call.rate.cutoff] (default = 0.95) |
− | MAXWARNINGS [NUMBER] (default = 20) | |
− | VERBOSE [ON|OFF] (default = 'OFF')
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− | LOGPVALUE [ON|OFF] (default = 'OFF')
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− | ANALYZE [HETEROGENEITY]
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− | CLEAR
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| | | |
− | Additional details on the [[METAL LOGPVALUE|LogPValue]] and [[METAL VERBOSE|Verbose]] commands are available. | + | Additional details on these options are [[Rare-Metal#QC_Options|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 variants.to.be.conditioned.upon] |
| + | Additional details for these options are [[Rare-Metal#Association_Methods|available]]. |
| | | |
− | SOURCE [FILENAME] | + | === Other Options for Performance and Amenities === |
| + | --labelHits [ON|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 are [[METAL SOURCE|available]]. | + | Additional details for these options are [[Rare-Metal#Other_Options|available]]. |