Support filtering incomplete penetrance in sample tree

docs/advanced/classification_trees.md

@@ -17,7 +17,7 @@ VIP contains default filtration strategies for variant-consequences as well as v
 The default decision tree to classify variant-consequences works as follows:
 
 1. Each variant-consequence is classified as `Benign`, `Likely Benign`, `VUS`, `Likely Pathogenic`, `Pathogenic` or `Remove`
-2. Variant-consequences classified as `Benign`, `Likely Benign` and `Remove` are removed
+2. Variant-consequences classified as `Benign`, `Likely Benign` and `Remove` are removed by default.
 
 ![Default classification tree](../img/GRCh38_decision_tree.png)
 
@@ -26,8 +26,8 @@ The default decision tree to classify variant-consequences works as follows:
 ### Variant-consequences (samples)
 The default decision tree to classify variant-consequences in the context of samples works as follows:
 
-1. Each variant-consequence-sample is classified as `U1` (usable: probably), `U2` (usable: maybe) and `U3` (usable: probably not)
-2. Variant-consequences classified as `U3` for all samples are removed
+1. Each variant-consequence-sample is classified as `U1` (usable: probably), `U2` (usable: maybe), `U3` (usable: probably not) and `U4` (usable: only in cases of suspected incomplete penetrance).
+2. Variant-consequences classified as `U3` and `U4` for all samples are removed by default.
 
 ![Default variant-sample classification tree](../img/sample_decision_tree.png)
 

resources/decision_tree_samples.json

@@ -41,11 +41,29 @@
         "value": 20
       },
       "outcomeTrue": {
-        "nextNode": "vim"
+        "nextNode": "only_IP"
       },
       "outcomeFalse": {
         "nextNode": "exit_u3"
       },
+      "outcomeMissing": {
+        "nextNode": "only_IP"
+      }
+    },
+    "only_IP": {
+      "type": "BOOL",
+      "description": "Only AD IP suitable for pedigree.",
+      "query": {
+        "field": "FORMAT/VI",
+        "operator": "contains_none",
+        "value": ["AR","AD","XLR","XLD","YL","MT","AR_C"]
+      },
+      "outcomeTrue": {
+        "nextNode": "vid_IP"
+      },
+      "outcomeFalse": {
+        "nextNode": "vim"
+      },
       "outcomeMissing": {
         "nextNode": "vim"
       }
@@ -68,6 +86,24 @@
         "nextNode": "exit_u2"
       }
     },
+    "vim_IP": {
+      "type": "BOOL",
+      "description": "Inheritance match",
+      "query": {
+        "field": "FORMAT/VIG",
+        "operator": "contains",
+        "value": "field:INFO/CSQ/Gene"
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_u4"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_u3"
+      },
+      "outcomeMissing": {
+        "nextNode": "exit_u4"
+      }
+    },
     "vid": {
       "type": "BOOL",
       "description": "Inheritance denovo",
@@ -86,6 +122,24 @@
         "nextNode": "exit_u2"
       }
     },
+    "vid_IP": {
+      "type": "BOOL",
+      "description": "Inheritance denovo",
+      "query": {
+        "field": "FORMAT/VID",
+        "operator": "==",
+        "value": 1
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_u1"
+      },
+      "outcomeFalse": {
+        "nextNode": "vim_IP"
+      },
+      "outcomeMissing": {
+        "nextNode": "exit_u2"
+      }
+    },
     "exit_u1": {
       "description": "Usable: probably",
       "type": "LEAF",
@@ -100,6 +154,11 @@
       "description": "Usable: probably not",
       "type": "LEAF",
       "class": "U3"
+    },
+    "exit_u4": {
+      "description": "Usable: in case of incomplete penetrance",
+      "type": "LEAF",
+      "class": "U4"
     }
   }
 }