Add pathogen-cluster-mutations command
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pathogen-cluster-mutations command
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Adds a new top-level pathogen-cluster-mutations command that allows users to pass a reference sequence, an alignment, and a table of cluster assignments and get a table of mutations found in each cluster at some minimum count and frequency. This is a direct port of the cluster_mutation.py script [1] from the cartography project. It exists as its own separate command so users (including us) can find mutations for any predefined genetic groups including clusters, Nextstrain clades, MCCs, Pango lineages, etc. Closes #20 [1] https://github.com/blab/cartography/blob/717deb1142e1a14f6b74c5a6e794e902dda4aa1c/notebooks/scripts/cluster_mutation.py
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Description
Adds a new top-level
pathogen-cluster-mutationscommand that allows users to pass a reference sequence, an alignment, and a table of cluster assignments and get a table of mutations found in each cluster at some minimum count and frequency.This is a direct port of the cluster_mutation.py script from the cartography project. It exists as its own separate command so users (including us) can find mutations for any predefined genetic groups including clusters, Nextstrain clades, MCCs, Pango lineages, etc.
Related issues
Closes #20