Hi everyone, I’m running the

nf-core/sarek

pipeline in germline mode on mouse data. It looks like the built-in mm10 reference from iGenomes only includes the 22 primary chromosomes (1–19, X, Y, MT). Could someone please confirm if this is expected? If I need unplaced/unlocalized contigs for my analysis, should I build and supply a custom reference genome instead? Thanks!

Unfortunately, for now that is the solution, we are working on another solution, but that takes time

thanks for your confirmation!