[GET-dev] Autoscores + Counsyl variants

[Tom Clegg]

Autoscores for all of the Counsyl variants are attached.

There were a few lines that look like they were corrupted by some
translation process (I ignored them):

",nsSNP8S
",nsSNP58Q
",nsSNP52W

Distribution of autoscores for counsyl variants:  (select
autoscore,count(variant_id) from counsyl_autoscore group by autoscore)

+-----------+-------------------+
| autoscore | count(variant_id) |
+-----------+-------------------+
| 0         |                33 |
| 1         |                 4 |
| 2         |               119 |
| 3         |                 4 |
| 4         |               129 |
+-----------+-------------------+

Distribution of autoscores for all variants:  (cut -f40 latest-flat.tsv |
tail -n +2 | sort -n | uniq -c)

  62304 0
   3993 1
  10473 2
   1512 3
   3378 4

Presumably *some* variants should be getting scores >4 -- I'll have to look
at this tomorrow (examples welcome).

The "in genetests?" contribution to the above autoscores is based on whether
the gene is *listed* in genetests, not whether its record indicates "test
available"... contrary to what I told Madeleine today.  I've fixed that just
now, and the scores are being recalculated.  (64 of the 836 genes in
genetests are "no test available")

Tom
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