add in missing alphamissence to annotations

PMBio · May 16, 2024 · d6a8782 · d6a8782
1 parent 3238e39
commit d6a8782
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/tests/deeprvat/test_data/training/config.yaml b/tests/deeprvat/test_data/training/config.yaml
@@ -194,6 +194,7 @@ training_data:
             - DeepRipe_plus_MBNL1_parclip
             - DeepRipe_plus_QKI_parclip
             - SpliceAI_delta_score
+            - alphamissense
         use_common_variants: False
         use_rare_variants: True
         verbose: True
@@ -234,6 +235,7 @@ training_data:
                     - DeepRipe_plus_MBNL1_parclip
                     - DeepRipe_plus_QKI_parclip
                     - SpliceAI_delta_score
+                    - alphamissense
                 thresholds:
                     MAF: "MAF < 1e-2"
                     CADD_PHRED:  "CADD_PHRED > 5"
@@ -312,6 +314,7 @@ data:
             - DeepRipe_plus_MBNL1_parclip
             - DeepRipe_plus_QKI_parclip
             - SpliceAI_delta_score
+            - alphamissense
         gene_file: example/protein_coding_genes.parquet
         use_common_variants: False
         use_rare_variants: True
@@ -352,6 +355,7 @@ data:
                     - DeepRipe_plus_MBNL1_parclip
                     - DeepRipe_plus_QKI_parclip
                     - SpliceAI_delta_score
+                    - alphamissense
                 thresholds:
                     MAF: "MAF < 1e-3"
                     CADD_PHRED:  "CADD_PHRED > 5"