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Cluster Investigation & Virus Epidemiology Tool
https://cov-lineages.org/resources/civet.html
GNU General Public License v3.0
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search for mutations of interest #157

Closed omarkr8 closed 2 years ago

omarkr8 commented 2 years ago

Just a question.

The papers says we can specify mutations (nucleotide and amino acid) to focus on the tree?

Which options are related to this? and what needs to be supplied? im guessing its possible to make a specific snipit figure to show just our loci of interest?

aineniamh commented 2 years ago

Ah, sorry I missed this issue before! Internally, civet will run scorpio and type each of your sequences in turn for the mutations of interest (so if you specified S:N501Y, it would check for them in your sequences). It then adds a column to the output metadata with the genotype at that point for each sequence and will annotate the tips of the output phylogeny with the genotype of each sequence. You can then colour the tree by the genotype as well to help highlight that SNP occurance accross your sequences.

An example of this can be found here: https://cov-lineages.org/resources/civet/civet_case_study_2.html