Like @eldariont mentioned before, the reference for bedtools is not formatted properly. I'm not sure what is happening, I tried using the different ways of citing (DOI, pubmed, tag) but none worked. We should try to fix this before submitting.
In the end it was a sneaky problem with the @ that wasn't a proper @. Maybe it was copy-pasted from somewhere. b7e940b083ed713f71bffe52ec525860a4d861b2 fixes it.
Like @eldariont mentioned before, the reference for bedtools is not formatted properly. I'm not sure what is happening, I tried using the different ways of citing (DOI, pubmed, tag) but none worked. We should try to fix this before submitting.