samtools-mpileup(1) on Linux
The text 7a40abd21e93, as Debian 12 (Bookworm) shipped it.
produces "pileup" textual format from an alignment
Flags it lists
-
--count-orphans -
--disable-overlap-removal -
--ignore-RG -
--ignore-overlaps-removal -
--illumina1.3+ -
--no-BAQ -
--no-output-del -
--no-output-ends -
--no-output-ins -
--no-output-ins-mods -
--output -
--output-BP -
--output-BP-5 -
--output-MQ -
--output-QNAME -
--output-mods -
--redo-BAQ -
--reverse-del -
-6 -
-A -
-B -
-E -
-M -
-O -
-R -
-X -
-a -
-o -
-s -
-x