Creating a BED file of unplaced contigs from a reference genome.

Question

[milesandersonmn]

I need to include a BED file of unplaced contigs in a reference genome for a structural variant pipeline. The problem is I don't know how to identify unplaced contigs from my reference files and then calculate their length for the BED coordinates. We have chromosome level scaffolding in our reference genome as well as over 10,000 other scaffolds, however I don't know if they are mapped or not. I would assume I could just extract all scaffold names but the chromosome scaffolds, and then calculate their lengths?

Does anyone know of a simple tool or way to do this?