How can i obtain all the regions reads hit. (in duplication region)

[liukeweiaway]

If a reads hit multiple regions, can i use bwa obtain these regions in sam/bam file?

[nicolo-tellini]

the option -a: output all found alignments for single-end or unpaired paired-end reads. These alignments will be flagged as secondary alignments. The XA tag gives additional info about multiple locations. see

bwa/README-alt.md

Line 76 in 79b230d

potential hits reported in the XA tag, lifts ALT hits to the chromosomal

[liukeweiaway]

the option -a: output all found alignments for single-end or unpaired paired-end reads. These alignments will be flagged as secondary alignments. The XA tag gives additional info about multiple locations. see

bwa/README-alt.md

Line 76 in 79b230d

potential hits reported in the XA tag, lifts ALT hits to the chromosomal

The answer help he a lot! Thanks