Orphan read in PE seq
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 !
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