Hi. @Gisela Gabernet . I was wondering if Airrflow recognizes indels and uses them to count mutations in a clone. Since for a clone-the V, D and the junction lengths have to be the same, how are sequence lengths difference due to indels handled? https://changeo.readthedocs.io/en/stable/methods/clustering.html. Thanks

Hi Aditee, yes if there is an insertion in the junction region, this sequence will be assigned to a different clone as the junction length will not be the same. So far as airrflow and the underlying Immcantation tools do not recognize or annotate indels. Changeo MakeDB removes the insertions from the V region in the "sequence_alignment" column, as the Immcantation framework tools need sequences without insertions to be able to match with the IMGT numbering. Additionally, insertions inside the junction region would be very difficult to recognize as D gene assignments are often ambiguous due to the short D gene length and the insertions there could be also attributed to N/P nucleotides.

Thanks a lot for the information.