[Bio-bwa-help] BWA-MEM Paired End mode

[Juan D. M. C. <jdm...@gm...>]

Hi all,
According to a previous mail I understand that if a read has multiple
optimal alignments on a reference, bwa will choose one of them and will
report it.
Now, what happens with the read pair information? Does it use it to report
the most likely position according to the insert size?
If the mate read has also multiple optimal alignments, are both reads
discarded?
And what happens if one of the mates cannot be mapped to the reference, are
both discarded? or are both reported as unmapped?

Look forward to hearing from you.

Best regards everyone,

Juan Montenegro