The authors use MHC genes as an example, but these analyses may also be relevant for following alleles across homeologs.
They suggest “ultra-deep” sequencing:
“An alternative approach that utilizes ultra-deep sequencing (hundreds to thousands of sequences per amplicon) to reconstruct genotypes and applies statistical methods on the sequencing depth to separate alleles from artefacts appears to be more robust. “
Critical review of NGS analyses for de novo genotyping multigene families
Jackie Lighten, Cock van Oosterhout, and Paul Bentzen