I'm currently struggling with structural variant calling.
I would like to call those structural variants for all samples in my population of haploid fungi (around 100).
My aim is to cross the results of all samples to get absence/presence polymorphisms of all called variants.
Would anyone know a tool that is able to call variants on all samples, and then cross the results to have only one file with SVs presence/absence for all samples?
Thanks in advance for your help
EDIT : I've eventually been using Delly2, which can handle multi-sample calling