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genmod is a tool for annotating and analyzing vcf files. By default variants will be annotated from the human refGene database but alternative annotations can be built with genmod build_annotations. If a pedigree file is provided the genetic models followed for each variant will be annotated on family level. If 1000G, ExAC or CADD files are provided theses will also be annotated, see genmod annotate.
genmod uses multithreading to annotate variants and operates on whole exom data in minutes and whole genome data in a few hours.