From e43eace9e5ef13f128bf36e413883ff8fcd3c9bf Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Fri, 18 Feb 2022 13:36:09 -0800 Subject: [PATCH] Update bwa.1 --- bwa.1 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bwa.1 b/bwa.1 index d30ac33..eefb235 100644 --- a/bwa.1 +++ b/bwa.1 @@ -154,8 +154,8 @@ batch of reads. The BWA-MEM algorithm performs local alignment. It may produce multiple primary alignments for different part of a query sequence. This is a crucial feature -for long sequences. However, some tools such as Picard's markDuplicates does -not work with split alignments. One may consider to use option +for long sequences. However, some tools may not work with split alignments. +One may consider to use option .B -M to flag shorter split hits as secondary.