Add reason why 21987 is masked by default
@@ -107,6 +107,7 @@ mask:
# Specific sites to mask in the reference genome's coordinates.
# These are 1-indexed coordinates of sites that have been identified as prone to sequencing errors.
mask_sites: "21987 21846"
+ # 21987 is a problematic ARTIC V3 primer site. Impacts Delta & some 21L (Omicron) descendants
# Depending on how you define focal and contextual inputs, the same strains may
# appear in both inputs. This option tells the workflow not to throw an error
