How are genes with frameshift mutations/INDELS handled?

[sydelstan]

Hello,

I find that genes with frameshift mutations are often treated as pangenome elements. Is there a way to correct for this? For example, if 32 of 90 strains carry gene X with an insertion that causes a frameshift mutation, I found that the Roary output will indicate that 90 strains carry gene X, but 32 strains carry an additional gene Y as part of the genome, even though gene Y is a truncated version of gene X.