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Gens integration

Gens is a interactive web-based tool to visualize copy number profiles using wgs data. It display the normalized read depth and alternative allele frequency in relation to transcripts, variants and previously annotated marker panels.

Setup

To avoid dependency conflicts Gens should be installed in an environment separate from scout. Install Gens according to the instructions on the tool homepage.

Config Parameters

  • GENS_HOST: The IP or hostname of the server where Gens is hosted.
  • GENS_PORT: Port number where gens is hosted (optional).
  • GENS_VERSION: Gens major version (Optional int). If a host but no version is provided, Scout attempts to find the version via gens API call at first web interface use (after a user has authenticated).

Configure Gens integration

In the scout config config.py provide the connection settings like:

GENS_HOST = "127.0.0.1"
GENS_PORT = 5001
GENS_VERSION = 4

Result

Now scout will display a button called "Gens" in the case view and in the variant view for structural variants.
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