Finding sequences not in the reference genome

[inti]

Hi, What is the best way to find sequences that are present in resequenced individuals but are missing from the reference genome? I have a reference renome for a plant specie and a few tens of 5-10x coverage sequence individuals and I want to find DNA sequence present on the individuals that is missing from the reference. I have seen this is possible to do with cortex_var but I am unsure how it could be done with mccortex.

Thanks in advance