I am working on compiling a list of all tools/software on Bioconda that use the BED file format as input. The tool doesn't have to only use BED as input, but can use BED in conjunction with other types such as BAM or VCF as well.
I have started a Google Sheet here with what I've found so far. Any suggestions here or comments on the Google Sheet would be amazing.
Thanks a lot for your help!