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.
If the lineage is provided, find_sample_size() in vcf2gvf.pylooks for whichever line in the stats file starts with the lineage name. This could cause an error if the lineage it looks for is the partial/beginning of another lineage name. Need to rewrite the string matching to include the whole lineage name, excluding the file extension.
If the lineage is provided,
find_sample_size()invcf2gvf.pylooks for whichever line in the stats file starts with the lineage name. This could cause an error if the lineage it looks for is the partial/beginning of another lineage name. Need to rewrite the string matching to include the whole lineage name, excluding the file extension.