r1281: with --write-junc, ignore aln with low mapQ

2026-10-05 01:08:11 +08:00 · 2025-04-17 21:46:54 -04:00
parent df9e650346
commit b58b97423a
3 changed files with 3 additions and 2 deletions
@@ -552,6 +552,7 @@ Output splice junctions in 6-column BED: contig name, start, end,
 read name, score and strand. Score is the sum of donor and acceptor scores,
 where GT gets 3, GC gets 2 and AT gets 1 at donor sites,
 while AG gets 3 and AC gets 1 at acceptor sites.
+Alignments with mapping quality below 10 are ignored.
 .TP
 .BI --pass1 \ FILE
 Junctions BED file outputted by