# Annotation
NOTE
This documentation is a work in progress and is incomplete.
Please contact developers for more details.
# Included transcripts
Configure types transcripts to include using regex, e.g. NM_.*
for RefSeq transcripts.
- File:
ella_config.yml
(set byELLA_CONFIG
env variable) - Key:
transcripts.inclusion_regex
# Frequencies
Settings related to population frequency annotation.
- File:
ella_config.yml
(set byELLA_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
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