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 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:
Filename | Filesize | Harvard Dataverse |
---|---|---|
Chr1 CSV | 31.2 GB | Download |
Chr2 CSV | 32.5 GB | Download |
Chr3 CSV | 26.6 GB | Download |
Chr4 CSV | 25.3 GB | Download |
Chr5 CSV | 24.2 GB | Download |
Chr6 CSV | 23.0 GB | Download |
Chr7 CSV | 21.2 GB | Download |
Chr8 CSV | 19.4 GB | Download |
Chr9 CSV | 16.3 GB | Download |
Chr10 CSV | 18.0 GB | Download |
Chr11 CSV | 18.2 GB | Download |
Chr12 CSV | 18.0 GB | Download |
Chr13 CSV | 13.1 GB | Download |
Chr14 CSV | 12.2 GB | Download |
Chr15 CSV | 11.3 GB | Download |
Chr16 CSV | 11.2 GB | Download |
Chr17 CSV | 11.3 GB | Download |
Chr18 CSV | 10.5 GB | Download |
Chr19 CSV | 8.0 GB | Download |
Chr20 CSV | 8.6 GB | Download |
Chr21 CSV | 5.1 GB | Download |
Chr22 CSV | 5.2 GB | Download |
Chr1 SQL | 29.1 GB | Download |
Chr2 SQL | 30.3 GB | Download |
Chr3 SQL | 24.8 GB | Download |
Chr4 SQL | 23.5 GB | Download |
Chr5 SQL | 22.5 GB | Download |
Chr6 SQL | 22.7 GB | Download |
Chr7 SQL | 19.8 GB | Download |
Chr8 SQL | 18.1 GB | Download |
Chr9 SQL | 15.2 GB | Download |
Chr10 SQL | 16.8 GB | Download |
Chr11 SQL | 17.0 GB | Download |
Chr12 SQL | 16.8 GB | Download |
Chr13 SQL | 12.2 GB | Download |
Chr14 SQL | 11.4 GB | Download |
Chr15 SQL | 10.5 GB | Download |
Chr16 SQL | 10.4 GB | Download |
Chr17 SQL | 10.6 GB | Download |
Chr18 SQL | 9.7 GB | Download |
Chr19 SQL | 7.5 GB | Download |
Chr20 SQL | 8.1 GB | Download |
Chr21 SQL | 4.8 GB | Download |
Chr22 SQL | 4.8 GB | Download |