How to set bwa to resport all the best repeat hit?

[genelab]

Hello all,
How to set bwa to resport all the best repeat hits? The default is only to report the random choosed one from all the best repeat hits.
All reply will be great appreciated. thx

[john_mu]

I thought it did this by default?

from the manual:

By default, if the best hit is no so repetitive (controlled by -R), BWA also finds all hits contains one more mismatch; otherwise, BWA finds all equally best hits only. Base quality is NOT considered in evaluating hits. In paired-end alignment, BWA pairs all hits it found. It further performs Smith-Waterman alignment for unmapped reads with mates mapped to rescue mapped mates, and for high-quality anomalous pairs to fix potential alignment errors.

[genelab]

I thought it did this by default?

from the manual:

By default, if the best hit is no so repetitive (controlled by -R), BWA also finds all hits contains one more mismatch; otherwise, BWA finds all equally best hits only. Base quality is NOT considered in evaluating hits. In paired-end alignment, BWA pairs all hits it found. It further performs Smith-Waterman alignment for unmapped reads with mates mapped to rescue mapped mates, and for high-quality anomalous pairs to fix potential alignment errors.

Thanks for your kindly reply.
This may be the default setting of "bwa aln", however, when i use 'bwa samse' to convert the result.sai ,generated by 'bwa aln', to sam format, the read in the sam result hava at most one hit.

form the samse part of manual:
Samse generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen

[john_mu]

If I remember correctly, it outputs the other ones in the "XA" tag at the end of the line.

if you set the -n option to a high number, you should get most of the hits.

I think the hits are chosen randomly in this case because all the repetitive hits are equally good.