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:

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

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