Merge pull request #43 from Clinical-Genomics/v0.8.1

V0.8.1
Clinical-Genomics · Nov 15, 2021 · cf10d92 · cf10d92
2 parents 9906571 + 84c9760
commit cf10d92
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Showing 6 changed files with 21 additions and 17 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,10 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 ## [x.x.x]
 
+## [0.8.1]
+Fix DAB1 pathologic repeat unit name
+Update POLG coords, quite a bit on hg38
+
 ## [0.8.0]
 Off by one error on PathogenticMin output. All affected have at least been cautioned pre_mutation with proper size.
 Added script to check HGNCId-symbol correspondence against genenames.org.

diff --git a/stranger/__version__.py b/stranger/__version__.py
@@ -1 +1 @@
-__version__ = '0.8.0'
+__version__ = '0.8.1'
diff --git a/stranger/resources/variant_catalog_grch37.json b/stranger/resources/variant_catalog_grch37.json
@@ -370,7 +370,7 @@
         ],
         "VariantId": [
             "DAB1_ATTTT1",
-            "DAB1_ATTTC",
+            "DAB1",
             "DAB1_ATTTT2"
         ],
         "PathologicRegion": "1:57832725-57832780",
@@ -1008,10 +1008,10 @@
         "LocusStructure": "(CTG)*TTG(CTG)*",
         "VariantType": ["Repeat","Repeat"],
         "VariantId": ["POLG_I", "POLG_II"],
-        "ReferenceRegion": ["15:89876820-89876826",
-                            "15:89876829-89876859"],
+        "ReferenceRegion": ["15:89876821-89876826",
+                            "15:89876830-89876859"],
         "NormalMax": 15,
         "PathologicMin": 10000,
-        "PathologicRegion": "15:89876829-89876859"
+        "PathologicRegion": "15:89876830-89876859"
     }
 ]
diff --git a/stranger/resources/variant_catalog_grch38.json b/stranger/resources/variant_catalog_grch38.json
@@ -389,7 +389,7 @@
         ],
         "VariantId": [
             "DAB1_ATTTT1",
-            "DAB1_ATTTC",
+            "DAB1",
             "DAB1_ATTTT2"
         ],
         "PathologicRegion": "1:57367053-57367108",
@@ -1217,10 +1217,10 @@
       "SourceId": "CMMS",    
       "VariantId": ["POLG_I", "POLG_II"],
       "LocusStructure": "(CTG)*TTG(CTG)*",
-      "ReferenceRegion": ["15:89833580-89833586",
-                          "15:89833589-89833628"],
+      "ReferenceRegion": ["15:89333590-89333595",
+                          "15:89333599-89333628"],
       "NormalMax": 15,
       "PathologicMin": 10000,
-      "PathologicRegion": "15:89833589-89833628"
+      "PathologicRegion": "15:89333599-89333628"
     }
 ]
diff --git a/stranger/resources/variant_catalog_hg19.json b/stranger/resources/variant_catalog_hg19.json
@@ -370,7 +370,7 @@
         ],
         "VariantId": [
             "DAB1_ATTTT1",
-            "DAB1_ATTTC",
+            "DAB1",
             "DAB1_ATTTT2"
         ],
         "PathologicRegion": "chr1:57832725-57832780",
@@ -1008,10 +1008,10 @@
         "LocusStructure": "(CTG)*TTG(CTG)*",
         "VariantType": ["Repeat","Repeat"],
         "VariantId": ["POLG_I", "POLG_II"],
-        "ReferenceRegion": ["chr15:89876820-89876826",
-                            "chr15:89876829-89876859"],
+        "ReferenceRegion": ["chr15:89876821-89876826",
+                            "chr15:89876830-89876859"],
         "NormalMax": 15,
         "PathologicMin": 10000,
-        "PathologicRegion": "chr15:89876829-89876859"
+        "PathologicRegion": "chr15:89876830-89876859"
     }
 ]
diff --git a/stranger/resources/variant_catalog_hg38.json b/stranger/resources/variant_catalog_hg38.json
@@ -389,7 +389,7 @@
         ],
         "VariantId": [
             "DAB1_ATTTT1",
-            "DAB1_ATTTC",
+            "DAB1",
             "DAB1_ATTTT2"
         ],
         "PathologicRegion": "chr1:57367053-57367108",
@@ -1217,10 +1217,10 @@
       "SourceId": "CMMS",    
       "VariantId": ["POLG_I", "POLG_II"],
       "LocusStructure": "(CTG)*TTG(CTG)*",
-      "ReferenceRegion": ["chr15:89833580-89833586",
-                          "chr15:89833589-89833628"],
+      "ReferenceRegion": ["chr15:89333590-89333595",
+                          "chr15:89333599-89333628"],
       "NormalMax": 15,
       "PathologicMin": 10000,
-      "PathologicRegion": "chr15:89833589-89833628"
+      "PathologicRegion": "chr15:89333599-89333628"
     }
 ]