Calculating unmutated frequency in IgDiscover output

[scharch]

According to the docs here, orgdbstats should be run on the unzipped filtered.tsv. However, the sequence_alignment field output by IgDiscover is ungapped, which results in ogrdbstats assigning 0 unmutated_sequences for all alleles, even though IgDiscover itself thinks that about 20% of the sequences are unmutated. Any way around this?

This is a non-model species. I've manually gapped the "reference" (such as it is) database, but I can't do that for the bulk sequencing data and I'm not finding an annotation tool that does gaps and can handle non-model species.