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− | to be constructed ... | + | [[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 === |
| + | Options: |
| + | List of Studies : --studyName [] |
| + | Grouping Methods : --groupFile [], --annotatedVcf [], --annotation [], |
| + | --writeVcf |
| + | QC Options : --hwe [1.0e-05], --callRate [0.95] |
| + | Association Methods : --burden, --MB, --SKAT, --VT, --condition [] |
| + | Other Options : --labelHits, --correctGC, --prefix [], |
| + | --mapFile [../src/refFlat_hg19.txt], --maf [0.05], |
| + | --longOutput, --tabulateHits, --hitsCutoff [1.0e-06] |
| + | --altMAF |
| + | |
| + | === Describing Studies === |
| + | --studyName [your.list.of.studies.file] |
| + | |
| + | Additional details on this option is [[Rare-Metal#List_of_Studies_2|available]]. |
| + | |
| + | === Methods to Group Rare Variants === |
| + | |
| + | --groupFile [your.groups.file] |
| + | --annotatedVcf [your.annotated.vcf] |
| + | --annotation [nonsyn/stop/splice] |
| + | --writeVcf [ON|OFF] |
| + | |
| + | 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. |
| + | |
| + | === QC Options === |
| + | --hwe [hwe.pvalue.cutoff] (default = 1e-05) |
| + | --callRate [variant.call.rate.cutoff] (default = 0.95) |
| + | |
| + | Additional details on these options are [[Rare-Metal#QC_Options|available]]. |
| + | |
| + | === 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]]. |
| + | |
| + | === 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 for these options are [[Rare-Metal#Other_Options|available]]. |