To use STAR alignment tool, it is recommended that the annotation file includes un-placed and un-localized scaffolds while excluding patches and alternative haplotypes (in page 5 of http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STAR.posix/doc/STARmanual.pdf).
Ensembl annotation seems to have a file 'Homo_sapiens.GRCh38.92.chr_patch_hapl_scaff.gtf.gz' containing both un-placed scaffolds and patches (in here). But neened with unplaced scaffolds and NO patches. Which of these files is that? Or can it be found somewhere else?
And concerning the genome sequence file: Does the primary assembly include un-placed scaffolds?