Importing Data from dbGaP and SRA

The Genetic Analysis Center at the University of Washington has developed fetch-dbgap-files, an open-source tool designed to automate and streamline the retrieval of dbGaP-authorized files, making it easier to bring external data into AnVIL for analysis.

Key Features of fetch-dbgap-files

fetch-dbgap-files is a Python-based tool that facilitates seamless retrieval of files from dbGaP by leveraging the dbGaP File Selector. The tool is designed to handle the download process robustly, retrying failed downloads to ensure completeness. It supports both local execution via a Python script and cloud-based execution via a WDL workflow, which is available on Dockstore.

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