This tool takes an input VCF file and outputs a VCF file with renamed contigs. For example chr1 -> 1. This can be useful in a pipeline where tools have different naming standards for contigs.


For documentation and manuals visit our page.


ReplaceContigsVcfFile 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 ReplaceContigsVcfFile, please use the github issue tracker or contact the SASC team directly at: [email protected].