BWA, how to to suppress BWA to output suboptimal alignments

[hui_shi]

Hello everyone,

Is there a way to suppress BWA to output all suboptimal alignments, as shown in "X1" tag. All I need is is the alignment shown for the "X0" tag.

Some of my multi-mapped read had only 8 "best alignments", but over 10,000 "suboptimal alignments". All I want is just these 8 "best alignments", but BWA appears to write all over ten thousand alignment locations. This makes the alignment to run much slower, and takes a lot of hard drive space.

Best regards,

Hui

[hui_shi]

Thanks everyone, I seems to already find the way:

Using the '-R' command in the BWA "aln" seems to do the job.
e.g.

bwa aln -t 10 -R 1 <fasta> <fastq.gz> > <.sai>

Best regards,

Hui