Feature #473
closedImplement auto-scoring mechanism
Description
Remaining to do:
- "within 1 base of a splice site" test
- "indel in a coding region" and "...with frame shift" tests
Updated by Madeleine Ball almost 14 years ago
See discussion: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 >= 1.5Gene-specific lists (max of 2 points):
+1 if in GeneTests
another +1 (+2 total) if in a GeneReviews gene
Updated by Madeleine Ball almost 14 years ago
- 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.
Updated by Madeleine Ball almost 14 years ago
N.B. this is not so much a "robot" since it is not editing the page.
Updated by Tom Clegg almost 14 years ago
Autoscoring code:
The score shows up in an "autoscore" column in latest-flat.tsv, and in the "in silico" section.
The "within 1 base of a splice site" and "indel in a coding region" tests are not implemented yet.
Updated by Ward Vandewege about 13 years ago
- Project changed from 19 to GET-Evidence
- Category deleted (
GET-Evidence)
Updated by Madeleine Ball about 13 years ago
- 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".