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Integrate VAFator to annotate mutations with Variant Allele Frequency and subsequently classify them into clonal, intrahost or low frequency mutations.
Remove unnecessary --chromosome parameter, this is now inferred from the reference.
Transform iVar output table into VCF format and postprocess it similarly to other VCFs.
Conda dependencies are now modular which minimises collisions of dependencies.
Improve automated tests.
Support for other virus than SARS-CoV-2 is now tested!