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.
Code should run as is (unless fillna("n/a") for nt_name and aa_name has broken something downstream I haven't anticipated). Delins nt-level names still need to be parsed into HGVS (I'll work on this after Oc/Or tomorrow); these and any other unrecognized names will be called "n/a" in the GVF for now.
The HGVS name translations for HV.1.6.annotated.vcf are captured in this Google Sheet, to be reviewed again in the morning.
Issue was with incorrect use of
apply().Code should run as is (unless
fillna("n/a")fornt_nameandaa_namehas broken something downstream I haven't anticipated). Delins nt-level names still need to be parsed into HGVS (I'll work on this after Oc/Or tomorrow); these and any other unrecognized names will be called "n/a" in the GVF for now.The HGVS name translations for
HV.1.6.annotated.vcfare captured in this Google Sheet, to be reviewed again in the morning.