Figure 2. Exemplary cases that should be considered during genotyping.

(A) Primer sequences need clipping to call true variants (red) and not mask them via reference bases (blue). (B) Early primer clipping may result in missed deletions due to algorithmic soft clipping (primer sequence in light gray). (C) Genotyping parameters must be carefully set to reliably call different variant cases and represent them in the final consensus. CoVpipe2 puts primer clipping after the mapping step to prevent B) and implements carefully chosen default parameters for robust genotyping also of mixed variants, C).