Here is what the docs say:
-t FILE This file is TAB-delimited. Each line must contain the reference name and the length of the reference, one line for each distinct reference; additional fields are ignored. This file also defines the order of the reference sequences in sorting. If you run ‘samtools faidx <ref.fa>’, the resultant index file <ref.fa>.fai can be used as this <in.ref_list> file.
I guess that tells me how to use it. But I'm wondering what the purpose is? What do people use this option for exactly? And what does it do?