Detect deletion between gene and pseudogenes

[keenhl]

We are trying to detect a deletion using Nanopore long read data. We think that the size of the deletion is something around 10-15 kb in size, although we are not sure. We have used both minimap and winnowmap for the alignment and sniffles for the variant calling. We have not been able to detect the deletion.

We believe that this difficulty might be attributable to the fact that the deletion is near a gene and its highly homologous pseudogene. We have only used standard parameters thus far. Are there parameters that would make sense to alter for this case? Is there something completely different in terms of our alignment strategy that we should be doing here?

Thanks for your help,