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Update bwa.1

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Nils Homer 2022-02-18 13:36:09 -08:00 committed by GitHub
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@ -154,8 +154,8 @@ batch of reads.
The BWA-MEM algorithm performs local alignment. It may produce multiple primary 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 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 for long sequences. However, some tools may not work with split alignments.
not work with split alignments. One may consider to use option One may consider to use option
.B -M .B -M
to flag shorter split hits as secondary. to flag shorter split hits as secondary.