Orphan read in PE seq

Question

[cmat34]

Hi !

I do variant calling with samtools mpileup, and i see there is an option '-A' which doesn't skip the orphan reads.

I have many orphan read marked in my bam files so I would like to know wether I can consider them or not ?

Also, do you know what are the parameters generating orphan read during a MiSeq PE sequencing ?

Thank you very much for your answer !