Question: If cells have the same CDR3, but different annotated genes in the chains, will they be called as different clonotypes?
Answer: No. Two cells are merged into a clonotype if the nucleotide sequences of the CDR3 of all productive chains in the cells are an exact match. The annotated genes in the chains are not considered for clonotype grouping at this time. Non-productive chains are also not considered for clonotype grouping.
For example, in the image below, Cell-1 and Cell-3 have different V genes for TRA chain. However, if the CDR3 nucleotide sequences are identical between Cell-1 and Cell-3 for both chains, they will be merged into a clonotype.