SACGF / SACGF/variantgrid

Variant ranking / prioritisation / ACMG auto-classification

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#154 5 comments 0 reactions 0 assignees View on GitHub
ACMG classification
Dominant language
Python
Stars
30
Forks
3
Avg merge
9h 22m
Merged PRs (30d)
40

Description

We have no way to prioritise variants within an analysis node. This would be good to reduce classification work on medical scientists.

ACMG classifications have 5 levels of clinical significance, but underneath that is a score from criteria weights - so I think using the score from an an ACMG classifier is also a variant prioritiser - hence moving all issues together here.

Personally, I'd much rather use an existing tool, though that may eg only work on default VEP fields, not all the information we have (though we could extend it)

Contributor guide

No contributing guide indexed for this repository

Research direction

Start at the analysis node and review the existing ACMG classification flow, including how classifier scores and default VEP fields are handled. Clarify whether to integrate an existing prioritisation tool or extend it for the available variant data; done means an agreed design and a working prioritisation path within an analysis node.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Quiet
Clarity
Needs clarification
Newbie friendliness
35/100

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