Annotation

NOTE

This documentation is a work in progress and is incomplete.

Please contact developers for more details.

• Included transcripts
• Frequencies
  • Groups
  • View
• Consequence
• Custom annotation

Included transcripts

Configure types transcripts to include using regex, e.g. NM_.* for RefSeq transcripts.

• File: ella_config.yml (set by ELLA_CONFIG env variable)
• Key: transcripts.inclusion_regex

Frequencies

Settings related to population frequency annotation.

• File: ella_config.yml (set by ELLA_CONFIG env variable)
• Key: frequencies

Groups

The key frequencies.groups defines which data should be in the external and internal frequency groups. Note that this also determines which groups can be used in the frequency filter and ACMG frequency configuration.

View

The key frequencies.view defines how frequency data should be shown.

Subkey	Explanation	Values
groups	Define how to group frequency annotation data.
precision	Float precision (for strings).	[integer]
scientific_threshold	Convert to scientific notation for frequencies below 10^-[x].	[integer]
indications_threshold	Define max threshold to show indications from internal database (depends on how the internal database is set up).	[integer]
[translations]	Define key to be used to link/lookup other sources of information.

Consequence

Define order of severity for transcript consequences given by VEP (high to low). This is used for searching for "worse consequence".

• File: /src/api/config/config.py
• Key: config.transcripts.consequences

Custom annotation

[TODO]

• Key: custom_annotation