The man pages lists --threads as equivalent to -@, but it's not actually supported by the code.
--- doc/samtools-index.1.orig 2023-06-28 13:24:30 UTC
+++ doc/samtools-index.1
@@ -125,7 +125,7 @@ Write the output index to
.IR FILE .
(Currently may only be used when exactly one alignment file is being indexed.)
.TP
-.BI "-@, --threads " INT
+.BI "-@ " INT
Number of input/output compression threads to use in addition to main thread [0].
.SH AUTHOR
The man pages lists --threads as equivalent to -@, but it's not actually supported by the code.