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 index 462d19b5..47c7c252 100644 --- 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]