I am using trying to detect SV using Hydra-SV. I skip all the first 3 steps as described in the workflow as I used stampy for mapping which I assume is sensitive enough. So i extracted all the discordant read-pairs and use
dedupDiscordants.py script. But when I use
hydra -in sample.disc.deduped.bedpe -out sample.breaks -mld 400 -mno 1200
the output file is empty. I checked the input file, it is as described. Looking for some help.