The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples.
The tool pretty-prints json or yaml output of cojac cooc-mutbamscan.
Hint: The output (unless you select html format) is best viewed in spreadsheet software that understands linebreaks.