samtools(1) on Linux
The text daa116fe1d2f, as Debian 7 (Wheezy) shipped it.
Utilities for the Sequence Alignment/Map (SAM) format bcftools - Utilities for the Binary Call Format (BCF) and VCF
Flags it lists
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-1 -
-6 -
-A -
-B -
-D -
-E -
-F -
-G -
-H -
-I -
-N -
-Q -
-S -
-b -
-c -
-e -
-f -
-g -
-h -
-n -
-o -
-r -
-s -
-u -
-v