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[Maintenance] Update gene model annotation resources #1455

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3 tasks
dnil opened this issue Jun 24, 2024 · 0 comments
Open
3 tasks

[Maintenance] Update gene model annotation resources #1455

dnil opened this issue Jun 24, 2024 · 0 comments
Labels
Maintenance Something which needs to be updated

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@dnil
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dnil commented Jun 24, 2024

Task

Update VEP to v110: v104 annotation seen

Gene model annotations appear mildly dated: the list of missing HGNC id is fairly large when loading Balsamic cases to Scout.

2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 49427
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 49506
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 49508
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 49509
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 41684
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 33538
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 41733
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 41828
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 41849
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 25767
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 33994
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 34394
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 42835
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 10134
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 10138
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 42990
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 43556
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 27299
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 42993
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 27913
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 37075
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 29111
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 29192
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 45656
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 45684
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 37499
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46040
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46101
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46152
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46251
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46297
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46437
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46506
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46517
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46548
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 38375
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46737
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46784
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 14087
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46873
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46955
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 22405
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 47833
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 48021
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 39996
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 48216
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 48313
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 48316
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 48317
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 48318
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 48321
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 31975
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 31985
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 31996
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 32021
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 48477
2024-06-24 10:02:18 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 48479
2024-06-24 10:02:29 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 26322
2024-06-24 10:02:29 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 45696
2024-06-24 10:02:29 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46222
2024-06-24 10:02:29 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46376
2024-06-24 10:02:29 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46564
2024-06-24 10:02:29 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46627
2024-06-24 10:02:29 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46717
2024-06-24 10:02:29 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46846
2024-06-24 10:02:29 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 47531
2024-06-24 10:02:29 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 47651
2024-06-24 10:02:29 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 47809
2024-06-24 10:02:29 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 48148
2024-06-24 10:02:37 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 32822
2024-06-24 10:02:37 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 47367
2024-06-24 10:02:37 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 45642
2024-06-24 10:02:37 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 41577
2024-06-24 10:02:37 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 47777
2024-06-24 10:02:37 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 13392
2024-06-24 10:02:37 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46837
2024-06-24 10:02:37 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46875
2024-06-24 10:02:37 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 40838
2024-06-24 10:02:38 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 35375
2024-06-24 10:02:42 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 47532
2024-06-24 10:02:42 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 43437
2024-06-24 10:02:42 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 45692
2024-06-24 10:02:42 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 26418
2024-06-24 10:02:48 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 41345
2024-06-24 10:02:48 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 41656
2024-06-24 10:02:48 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 47926
2024-06-24 10:02:48 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46025
2024-06-24 10:02:48 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46119
2024-06-24 10:02:48 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46311
2024-06-24 10:02:48 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46455
2024-06-24 10:02:48 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46492
2024-06-24 10:02:48 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46698
2024-06-24 10:02:48 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46883
2024-06-24 10:02:48 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 38900
2024-06-24 10:02:58 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 33815
2024-06-24 10:02:58 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 37072
2024-06-24 10:02:58 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46029
2024-06-24 10:02:58 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46080
2024-06-24 10:02:58 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46177
2024-06-24 10:02:58 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46223
2024-06-24 10:02:58 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46228
2024-06-24 10:02:58 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46381
2024-06-24 10:02:58 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 30058
2024-06-24 10:02:58 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46658
2024-06-24 10:02:58 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46832
2024-06-24 10:02:58 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46871
2024-06-24 10:02:58 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 47059
2024-06-24 10:02:58 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 48033
2024-06-24 10:02:58 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 40183
2024-06-24 10:03:05 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 37072
2024-06-24 10:03:05 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 48033
2024-06-24 10:03:05 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46029
2024-06-24 10:03:05 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46080
2024-06-24 10:03:05 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 33815
2024-06-24 10:03:05 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46177
2024-06-24 10:03:05 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46223
2024-06-24 10:03:05 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46228
2024-06-24 10:03:05 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 40183
2024-06-24 10:03:05 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 30058
2024-06-24 10:03:05 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46658
2024-06-24 10:03:05 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46832
2024-06-24 10:03:05 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46871
2024-06-24 10:03:05 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 47059
2024-06-24 10:03:05 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 40183
2024-06-24 10:03:16 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 41495
2024-06-24 10:03:16 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 25933
2024-06-24 10:03:16 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46072
2024-06-24 10:03:16 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46075
2024-06-24 10:03:16 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 5162
2024-06-24 10:03:16 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46130
2024-06-24 10:03:16 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46135
2024-06-24 10:03:16 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46211
2024-06-24 10:03:16 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46788
2024-06-24 10:03:16 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 47255
2024-06-24 10:03:16 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 47548
2024-06-24 10:03:16 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 47742
2024-06-24 10:03:16 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 23262
2024-06-24 10:03:16 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 48026
2024-06-24 10:03:16 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 48265
2024-06-24 10:03:16 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 24033
2024-06-24 10:03:20 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 47742
2024-06-24 10:03:20 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 23262
2024-06-24 10:03:20 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46075
2024-06-24 10:03:20 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46130
2024-06-24 10:03:20 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46135
2024-06-24 10:03:20 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 48265
2024-06-24 10:03:20 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46788
2024-06-24 10:03:25 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 47557
2024-06-24 10:03:25 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46195
2024-06-24 10:03:25 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 27887
2024-06-24 10:03:25 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46328
2024-06-24 10:03:25 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 48411
2024-06-24 10:03:25 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46712
2024-06-24 10:03:25 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46786
2024-06-24 10:03:28 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 45648
2024-06-24 10:03:28 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 45718
2024-06-24 10:03:28 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46195
2024-06-24 10:03:28 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 27887
2024-06-24 10:03:31 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46096
2024-06-24 10:03:31 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46305
2024-06-24 10:03:31 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 42541
2024-06-24 10:03:31 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 42608
2024-06-24 10:03:31 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 42731
2024-06-24 10:03:31 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 42781
2024-06-24 10:03:31 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 40874
2024-06-24 10:03:31 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 49114
2024-06-24 10:03:33 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46629
2024-06-24 10:03:33 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 32358
2024-06-24 10:03:33 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46363
2024-06-24 10:03:35 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46383
2024-06-24 10:03:36 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 45635
2024-06-24 10:03:36 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46746
2024-06-24 10:03:36 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46755
2024-06-24 10:03:40 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 39555
2024-06-24 10:03:40 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46100
2024-06-24 10:03:40 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46110
2024-06-24 10:03:40 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46131
2024-06-24 10:03:40 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46242
2024-06-24 10:03:40 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46314
2024-06-24 10:03:40 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46544
2024-06-24 10:03:40 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 38387
2024-06-24 10:03:40 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46642
2024-06-24 10:03:40 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46685
2024-06-24 10:03:40 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46860
2024-06-24 10:03:40 hasta.scilifelab.se scout.build.variant.variant[62211] WARNING missing HGNC symbol for: 46882

Sampling a few indicates outdated gene models/symbols:

Screenshot 2024-06-24 at 10 09 51
Screenshot 2024-06-24 at 10 10 27

These may or may not have been of interest anyway: it includes some very disputable pseudogenes, tentative RNA-genes etc, so not flagging this as a bug.

Suggested approach

It would be proactively good to keep the annotation substrate in sync. See e.g. #1276.

Updating VEP from v104 to v110 or higher would also solve the known issue of annotating both ends of BNDs - see e.g. Ensembl/ensembl-vep#1399, Clinical-Genomics/MIP#581 and Clinical-Genomics/scout#4446.

Deviation

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Risk assessment

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  • Not needed

Risk assessment link

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System requirements assessed

  • Yes, I have reviewed the system requirements

Requirements affected

No response

Can be closed when

No response

Blockers

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@dnil dnil added the Maintenance Something which needs to be updated label Jun 24, 2024
@dnil dnil added this to BALSAMIC Jun 24, 2024
@github-project-automation github-project-automation bot moved this to Todo in BALSAMIC Jun 24, 2024
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