Database Management

db and ANNOVAR Database Management

db is the option to manage your ANNOVAR databases. First you need to download ANNOVAR.

First use

If you use TAPES to manage ANNOVAR databases for the first time you need to provide the location of your ANNOVAR folder using:
python3 tapes.py db -s -A /path/to/annovar/

This will create 2 useful files in the src folder : db_config.json and db_vcf.json in the src folder.

Simplified database download

You can download only the databases needed by TAPES using:
python3 tapes.py db -b --acmg -a hg19

Full database management

Using the file db_config.json, you can see which databases are downloaded and which are missing. To flag a database for download, open db_config.json using any editor and replace "MISSING" by "DOWNLOAD" or "DOWN". then run:
python3 tapes.py db -b -a hg38

The databases flagged for download will all be downloaded

Options

• -s --see_db|flag|See which databases are present in the ANNOVAR folder
• -b --build_db|flag| Download flagged databases
• --acmg |flag| Bypasses the db_config.json file and download only necessary databases for TAPES
• -a --assembly|string| Either hg19 or hg38 - default is hg19