Update nallo rank model

nallo/rank_model/grch38_rank_model_snvs_-v1.0-.ini

@@ -191,23 +191,23 @@
 
   [[common]]
     score = -12
-    lower = 0.1
+    lower = 0.02
     upper = 1.1
 
   [[intermediate]]
-    score = 0
-    lower = 0.05
-    upper = 0.1
+    score = 1
+    lower = 0.005
+    upper = 0.02
 
   [[rare]]
     score = 2
-    lower = 0.01
-    upper = 0.05
+    lower = 0.0005
+    upper = 0.005
 
   [[very_rare]]
     score = 3
     lower = 0
-    upper = 0.01
+    upper = 0.0005
 
 [gene_intolerance_score]
   category = gene_intolerance_prediction
@@ -302,7 +302,7 @@
 [most_severe_consequence]
   category = consequence
   data_type = string
-  description = Most severe consequence for this variant (vep110)
+  description = Most severe consequence for this variant (vep107)
   field = INFO
   info_key = most_severe_consequence
   record_rule = max
@@ -313,6 +313,11 @@
     priority = 6
     string = 'transcript_ablation'
 
+  [[feature_truncation]]
+    score = 8
+    priority = 5
+    string = 'feature_truncation'
+
   [[splice_acceptor_variant]]
     score = 8
     priority = 5
@@ -493,11 +498,6 @@
     priority = 2
     string = 'regulatory_region_variant'
 
-  [[feature_truncation]]
-    score = 1
-    priority = 2
-    string = 'feature_truncation'
-
   [[intergenic_variant]]
     score = 0
     priority = 0
@@ -719,20 +719,117 @@
 
   [[common]]
     score = -12
-    lower = 0.1
+    lower = 0.02
     upper = 1.1
 
   [[intermediate]]
-    score = 0
-    lower = 0.05
-    upper = 0.1
+    score = 1
+    lower = 0.005
+    upper = 0.02
 
   [[rare]]
     score = 2
-    lower = 0.01
-    upper = 0.05
+    lower = 0.0005
+    upper = 0.005
 
   [[very_rare]]
     score = 3
     lower = 0
-    upper = 0.01
+    upper = 0.0005
+
+[revel]
+  category = protein_prediction
+  csq_key = REVEL_score
+  data_type = float
+  description = Revel score prediction
+  field = INFO
+  info_key = CSQ
+  record_rule = max
+  separators = None
+
+  [[not_reported]]
+    score = 0
+
+  [[tolerated]]
+    score = 0
+    lower = 0
+    upper = 0.5
+
+  [[probably_damaging]]
+    score = 2
+    lower = 0.5
+    upper = 0.75
+
+  [[damaging]]
+    score = 5
+    lower = 0.75
+    upper = 1
+
+[dbnsfp_gerp++_rs]
+  category = conservation
+  csq_key = GERP++_RS
+  data_type = float
+  description = Gerp conservation score
+  field = INFO
+  info_key = CSQ
+  record_rule = max
+  separators = ',',
+
+  [[not_reported]]
+    score = 0
+
+  [[conserved]]
+    score = 1
+    lower = 2
+    upper = 10
+
+  [[not_conserved]]
+    score = 0
+    lower = 0
+    upper = 2
+
+[dbnsfp_phastcons100way_vertebrate]
+  category = conservation
+  csq_key = phastCons100way_vertebrate
+  data_type = float
+  description = phastCons conservation score
+  field = INFO
+  info_key = CSQ
+  record_rule = max
+  separators = ',',
+
+  [[not_reported]]
+    score = 0
+
+  [[conserved]]
+    score = 1
+    lower = 0.8
+    upper = 100
+
+  [[not_conserved]]
+    score = 0
+    lower = 0
+    upper = 0.8
+
+[dbnsfp_phylop100way_vertebrate]
+  category = conservation
+  csq_key = phyloP100way_vertebrate
+  data_type = float
+  description = Phylop conservation score
+  field = INFO
+  info_key = CSQ
+  record_rule = max
+  separators = ',',
+
+  [[not_reported]]
+    score = 0
+
+  [[conserved]]
+    score = 1
+    lower = 2.5
+    upper = 100
+
+  [[not_conserved]]
+    score = 0
+    lower = 0
+    upper = 2.5

nallo/rank_model/grch38_rank_model_snvs_-v1.0-.ini.md5

@@ -1 +1 @@
-9a8a11132c16243097f8295fa9606dc5  nallo/rank_model/grch38_rank_model_snvs_-v1.0-.ini
+02ef4dcad483922461290865f9ca163b  nallo/rank_model/grch38_rank_model_snvs_-v1.0-.ini

nallo/rank_model/grch38_rank_model_svs_-v1.0-.ini

@@ -37,32 +37,27 @@
   separators = ',',
 
   [[not_reported]]
-    score = 4
-
-  [[missing]]
-    score = 4
-    lower = -1
-    upper = 0
+    score = 6
 
   [[common]]
     score = -12
-    lower = 0.1
+    lower = 0.02
     upper = 1.1
 
   [[intermediate]]
-    score = 0
-    lower = 0.05
-    upper = 0.1
+    score = 1
+    lower = 0.005
+    upper = 0.02
 
   [[rare]]
     score = 2
-    lower = 0.01
-    upper = 0.05
+    lower = 0.0005
+    upper = 0.005
 
   [[very_rare]]
-    score = 3
+    score = 4
     lower = 0
-    upper = 0.01
+    upper = 0.0005
 
 [colorsdb]
   category = allele_frequency
@@ -74,32 +69,32 @@
   separators = ',',
 
 [[not_reported]]
-    score = 4
+    score = 6
 
   [[missing]]
-    score = 4
+    score = 6
     lower = -1
     upper = 0
 
   [[common]]
     score = -12
-    lower = 0.1
+    lower = 0.05
     upper = 1.1
 
   [[intermediate]]
-    score = 0
-    lower = 0.05
-    upper = 0.1
+    score = 1
+    lower = 0.005
+    upper = 0.05
 
   [[rare]]
     score = 2
-    lower = 0.01
-    upper = 0.05
+    lower = 0.0005
+    upper = 0.005
 
   [[very_rare]]
-    score = 3
+    score = 4
     lower = 0
-    upper = 0.01
+    upper = 0.0005
 
 [loqusdb]
   category = allele_frequency
@@ -111,32 +106,32 @@
   separators = ',',
 
   [[not_reported]]
-    score = 4
+    score = 6
 
   [[missing]]
-    score = 4
+    score = 6
     lower = -1
     upper = 0
 
-  [[common]]
+   [[common]]
     score = -12
-    lower = 0.1
+    lower = 0.05
     upper = 1.1
 
   [[intermediate]]
-    score = 0
-    lower = 0.05
-    upper = 0.1
+    score = 1
+    lower = 0.005
+    upper = 0.05
 
   [[rare]]
     score = 2
-    lower = 0.01
-    upper = 0.05
+    lower = 0.0005
+    upper = 0.005
 
   [[very_rare]]
-    score = 3
+    score = 4
     lower = 0
-    upper = 0.01
+    upper = 0.0005
 
 [sv_len]
   category = variant_length
@@ -180,6 +175,33 @@
     lower = -400
     upper = -1
 
+[gene_intolerance_score]
+  category = gene_intolerance_prediction
+  data_type = float
+  description = Gnomad gene intolerance prediction
+  field = INFO
+  info_key = most_severe_pli
+  record_rule = max
+  separators = None
+
+  [[not_reported]]
+    score = 0
+
+  [[low_intolerance]]
+    score = 0
+    lower = 0
+    upper = 0.90
+
+  [[medium_intolerance]]
+    score = 2
+    lower = 0.90
+    upper = 0.99
+
+  [[high_intolerance]]
+    score = 4
+    lower = 0.99
+    upper = 1.1
+
 [genetic_models]
   data_type = string
   description = The inheritance models followed for the variant
@@ -240,15 +262,14 @@
     string = 'XD_dn'
 
   [[not_reported]]
-    score = 0
+    score = 3
 
 [most_severe_consequence]
   category = consequence
   data_type = string
   description = Most severe consequence for this variant (vep107)
   field = INFO
-  csq_key = Consequence
-  info_key = CSQ
+  info_key = most_severe_consequence
   record_rule = max
   separators = ',', ':', '|',
 
@@ -257,6 +278,11 @@
     priority = 6
     string = 'transcript_ablation'
 
+  [[feature_truncation]]
+    score = 8
+    priority = 5
+    string = 'feature_truncation'
+
   [[splice_acceptor_variant]]
     score = 8
     priority = 5
@@ -437,11 +463,6 @@
     priority = 2
     string = 'regulatory_region_variant'
 
-  [[feature_truncation]]
-    score = 1
-    priority = 2
-    string = 'feature_truncation'
-
   [[intergenic_variant]]
     score = 0
     priority = 0