This tool corrects the reference alleles in a VCF file. Some tools switch the REF and ALT alleles when creating a vcf. This tool checks what the reference allele is at the given position. It then checks whether this matches up with the REF and ALT column and switches them if necessary.


For documentation and manuals visit our page.


CorrectRefAlleles is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of a pipeline, for example the SASC team's biowdl pipelines.

All tools in the BIOPET tool suite are Free/Libre and Open Source Software.


For any question related to CorrectRefAlleles, please use the github issue tracker or contact the SASC team directly at: [email protected].