Converting Chromosome Names

Here we make use of the useful resources from the Github repository ChromosomeMappings to convert chromosome names between different genome assemblies.

We provided a script to parse any tab-delimited file with the chromosome names. The script is located at convert_contig_names.py

python3 convert_contig_names.py <input_file> <mapping_file> <output_file> [<chromosome_column>]

By default, if the column number is not specified, the script will assume the first column contains the chromosome names. Alternatively, the column number can be specified as the fourth argument, which should be 1-indexed, i.e., the first column is 1.