search

cov-lineages / scorpio

serious constellations of reoccurring phylogenetically-independent origin
GNU General Public License v3.0
38 stars 4 forks source link

Mutation information #18

Closed santoshe1 closed 3 years ago

santoshe1 commented 3 years ago

Hello Scorpio Team,

Thank you for the such a great tool. I would like to know if we could get the information of which are the variations/mutations in addition to the count of ALT, REF or AMG variant counts from the scorpio results?

rmcolq commented 3 years ago

At the moment, no. Although there is the option to run scorpio haplotype -i <alignment> -c <constellation json file> and this will output a string for every sequence in the alignment which is essentially a concatenation of the calls for each mutation listed in order (puts - for reference by default X for missing/ambiguous/other, number of amino acid positions deleted and ? if insertion in definition as currently not supported)

santoshe1 commented 3 years ago

Thank you @rmcolq for the information :)