samtools-mpileup(1) on Linux
The text 9571063d9ba9, as Debian 11 (Bullseye) shipped it.
produces "pileup" textual format from an alignment
Flags it lists
-
--count-orphans -
--ignore-RG -
--ignore-overlaps -
--illumina1.3+ -
--no-BAQ -
--output -
--output-BP -
--output-MQ -
--output-QNAME -
--redo-BAQ -
--reverse-del -
-6 -
-A -
-B -
-E -
-O -
-R -
-X -
-a -
-o -
-s -
-x