Fixed alt_allele in insertions

BU-ISCIII · Aug 16, 2024 · 74a1de8 · 74a1de8
1 parent 3976ec8
commit 74a1de8
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/create_irma_vcf.py b/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/create_irma_vcf.py
@@ -745,7 +745,7 @@ def combine_indels(vcf_dictionary):
         if value["TYPE"] == "INS":
             if value["REF_POS"] in combined_vcf_dict:
                 if value["TYPE"] == combined_vcf_dict[value["REF_POS"]]["TYPE"]:
-                    NEW_ALT = value["ALT"].replace(value["REF"], "")
+                    NEW_ALT = value["ALT"][len(value["REF"]) :]
                     combined_vcf_dict[value["REF_POS"]]["ALT"] += NEW_ALT
                     combined_vcf_dict[value["REF_POS"]]["SAMPLE_POS"].append(
                         value["SAMPLE_POS"][0]