use of sensv with plant genomes

[fernanarr]

Hi! This is not an issue but a question. We are searching for structural rearrangements between two plant genomes, the parental and a derived one. We have attempted to use SenSV, unsuccessfully, as it defaults to using the human reference genome despite specifying the parental genome in the reference file, and providing mutant reads as fastq files. How can we identify the differences between the two genomes? What do we need to modify in SenSV options?

Thanks a lot in advance.

Regards