GET-Evidence

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

• http://lists.freelogy.org/mailman/private/get-dev/2010-May/000005.html

• 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.

Autoscoring code:

http://github.com/tomclegg/get-evidence/blob/d188d93fd7321cdd952443c338a6f14382e29a7c/public_html/lib/evidence.php#L776

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.