Merge pull request #1469 from BRCAChallenge/debug_spliceai_merge

Fixed bug that caused splice_ai and bayesdel scores to not be shown f…

Author: melissacline

pipeline/data_merging/bayesdel/add_bayesdel_scores_to_built_file.py

@@ -54,7 +54,7 @@ def main(vcf_parts, built_tsv, output):
     df_victor = victor_results_as_df(vcf_parts)
     df = pd.read_csv(built_tsv, sep='\t', keep_default_na=False)
 
-    df_merged = df.merge(df_victor, left_on='Genomic_Coordinate_hg38', right_on=coord_col, how='left')
+    df_merged = df.merge(df_victor, left_on='pyhgvs_Genomic_Coordinate_38', right_on=coord_col, how='left')
 
     # drop join key and write
     (df_merged.drop(columns=[coord_col]).

pipeline/splice_ai/add_splice_scores_to_built_file.py

@@ -80,7 +80,7 @@ def main(vcf, built_tsv, output):
     df_spliceai = spliceai_results_as_df(vcf)
     df = pd.read_csv(built_tsv, sep='\t', keep_default_na=False)
 
-    df_merged = df.merge(df_spliceai, left_on='Genomic_Coordinate_hg38', right_on=coord_col, how='left')
+    df_merged = df.merge(df_spliceai, left_on='pyhgvs_Genomic_Coordinate_38', right_on=coord_col, how='left')
 
     # drop join key and write
     (df_merged.drop(columns=[coord_col]).