Feature #473
closed
Implement auto-scoring mechanism
Added by Tom Clegg almost 14 years ago.
Updated about 13 years ago.
Description
Remaining to do:
- "within 1 base of a splice site" test
- "indel in a coding region" and "...with frame shift" tests
Autoscoring is split into three sections: computational,
variant-specific, and gene-specific, each 2 points for a max of 6
points.
Computational (max of 2 points):
If an non-synonymous substitution:
+1 for NBLOSUM >= 3,
another +1 (+2 total) if NBLOSUM = 10 (a nonsense mutation)
For all variants:
+1 if within 1 base of a splice site
(Trait-o-matic has splicing data, presumably it could spot these?)
Indels:
+1 for indel in coding region
another +1 (+2 total) if causes a frameshift (not a multiple of 3 in
coding region)
Variant-specific lists (max of 2 points):
+2 if in OMIM
+1 if in PharmGKB
+1 if in HuGENet
another +1 (+2 total) if HuGENet's OR >= 1.5
Gene-specific lists (max of 2 points):
+1 if in GeneTests
another +1 (+2 total) if in a GeneReviews gene
See discussion:
Two more requirements:
- Let's put the autoscore into the "Other in silico analyses" section.
- The GET-Evidence dump should also have an autoscore column.
Both of these are urgent for completion of the ticket.
N.B. this is not so much a "robot" since it is not editing the page.
- Project changed from 19 to GET-Evidence
- Category deleted (
GET-Evidence)
- Status changed from New to Closed
One way or another, autoscoring is done now. Ideally it'd be done by the php and python wouldn't have redundant and potentially disagreeing versions, but I consider this bug/request to be "done".
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