This tool takes an input GTF file and outputs a GTF 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 github.io page.
ReplaceContigsGtfFile 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.