FAVOR Annotator

FAVORannotator is an open source R program (GitHub) for performing offline functional annotation of whole-genome/ whole-exome sequencing (WGS/WES) studies using the FAVOR database. It combines the functional annotation data with the input genotype data (VCF) to create an all-in-one aGDS file. The aGDS format allows for both the genotype and functional annotation data to be contained in a single file.

It converts a genotype VCF input file into a GDS file, searches the variants in the GDS file using the FAVOR database for their functional annotations (in PostgreSQL), and then integrates these annotations into the GDS file to create an aGDS file. This aGDS file allows both genotype and functional annotation data to be stored in a single file.

FAVORannotator can be conveniently integrated into the STAARpipeline (GitHub | Paper), a rare variant association analysis tool for WGS/WES studies, to perform association analysis of large-scale genetic data.

FAVORannotator's database (containing 20 essential annotation scores) can be downloaded from the following links: