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===== From an Annotated VCF File =====
===== From an Annotated VCF File =====
* If --groupFile option is not specified, '''rareMETAL''' will look for an annotated vcf file as blue print for variants to group.
* If --groupFile option is '''NOT''' specified, '''rareMETAL''' will look for an annotated vcf file as blue print for variants to group.
* The annotated VCF file should be specified using --annotatedVcf option.
* The annotated VCF file should be specified using --annotatedVcf option.
* --annotation should be used with --annotatedVcf together when specific category of functional variants are of interest to be grouped. For example, if grouping nonsynonymous and splicing variants are of interests, the following should be included in command line:
* --annotation should be used with --annotatedVcf together when specific category of functional variants are of interest to be grouped. For example, if grouping nonsynonymous and splicing variants are of interests, the following should be included in command line:
