A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.
Note for the future: in this pull request, I changed it to merge the functional annotations into the GVF based on 'protein_symbol' and 'Name' matching. I think given these two it's not necessary to also match on 'alias', but for the future I will need to update the functional annotation file with .fillna("n/a") for the 'alias' column.
Note for the future: in this pull request, I changed it to merge the functional annotations into the GVF based on 'protein_symbol' and 'Name' matching. I think given these two it's not necessary to also match on 'alias', but for the future I will need to update the functional annotation file with .fillna("n/a") for the 'alias' column.