From d6a878201d61c19304ac58dfed749f4d3414f0ed Mon Sep 17 00:00:00 2001 From: Kayla Meyer Date: Thu, 16 May 2024 13:18:56 +0200 Subject: [PATCH] add in missing alphamissence to annotations --- tests/deeprvat/test_data/training/config.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tests/deeprvat/test_data/training/config.yaml b/tests/deeprvat/test_data/training/config.yaml index 54487298..233baf7e 100644 --- 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"