BioNano Genomics Access FSHD integration

BioNano Access Server Integration

Starting from Scout release 4.71 the software can be configured to fetch FSHD reports for individual samples from a BioNano Genomics Access server. Currently, a single user account is used for accessing all project samples. Depending on your setup, this user may need admin privileges to read all. We find that a read_only user account works well.

Basic configuration for BioNano Access Integration

Edit Scout config file adding the following parameters:

# BioNano Access Server extension
BIONANO_ACCESS = "https://bionano-access.scilifelab.se"
BIONANO_USERNAME = "USER"
BIONANO_PASSWORD = "PASS"

The server address https://bionano-access.scilifelab.se is an externally available URL

Adding BioNano Access project and sample to the case config

Scout will look up samples using the BioNano Access project- and sample keys given for the individual. The preferred way is by case config file, adding bionano_access project and sample fields to the individual (sample):

bionano_access:
    project: "230303_customer_projectA1"
    sample: "2023-12345"

The scout update individual command can alternatively be directly used to update individuals that are already loaded.

scout update individual -c internal_id -i ADM1059A2 bionano_access.project 230303_customer_projectA1
scout update individual -c internal_id -i ADM1059A2 bionano_access.sample 2023-12345

It is advised to give the original (not a copy) project and sample name, as this can cause issues on the API. A copy can still exist and be used to restrict project read credentials on the Access server web interface appropriately.

Results appear in Scout as a tab for each case, reachable from the case page for cases that have bionano_access project and sample configured for at least one individual. Results are not cached in Scout, but re-retrieved on page load.