megadepth(1) on Linux
The text a903bd8ef258, as Debian 13 (Trixie), Debian 12 (Bookworm) shipped it. The page shows this text now.
Quantification of genome coverage by DNA/RNA seqencing
Flags it lists
-
--add-chr-prefix -
--all-junctions -
--alts -
--annotation -
--auc -
--bigwig -
--bwbuffer -
--coverage -
--delta -
--distance -
--double-count -
--echo-sam -
--ends -
--fasta -
--filter-in -
--filter-out -
--frag-dist -
--gzip -
--head -
--help -
--include-n -
--include-softclip -
--junctions -
--keep-order -
--longreads -
--min-unique-qual -
--no-annotation-stdout -
--no-auc-stdout -
--no-coverage-stdout -
--no-index -
--num-bases -
--only-polya -
--prefix -
--print-qual -
--read-ends -
--require-mdz -
--sums-only -
--test-polya -
--threads -
--unsorted -
--version -
-h