I’m currently working on setting up a variant calling workflow using bcftools mpileup and wanted to incorporate a repeat annotation file (in BED or GTF format) to help with interpretation. I came across Ensembl’s assembly repeats page, which looks promising, but it’s not entirely clear on how or where to download.

Since the UCSC Genome Browser isn’t compatible with my current reference build, that option’s off the table for now, so I’m still exploring the best way to move forward.

Any ideas?