Annotate

genmod annotate

This command is for annotating variants in a vcf file. The variants will get different annotations based on the input to genmod annotate

• Regions will be annotated
• genetic models will be annotated is a ped file is provided
• allele frequencies will be annotated if a frequency file is provided (1000G or Exac)
• Cadd scores can be annotated if there are any cadd files provided

Regions

Each variants will be annotated with the regions (genes) that they overlap, the vcf key is Annotations. If there are no annotations directory given as input the default annotation in genmod/annotationswill be used. This default annotation is built from the human refGene dataset. A custom annotation can be built by using the genmod build_annotation command. By doing this it is possible to annotate any organism or use another set of human annotations.

Genetic Models