Hello,
In samtools v.1.1 mpileup takes the option "-x --ignore-overlaps" which is
described as "disable read-pair overlap detection". Could anyone clarify
what this means?
My guess/understanding is that overlapping read pairs are not double
counted when the mates overlap, unless -x is set. Is this correct?
In previous versions overlapping read pairs were instead double counted,
right?
Thanks
Dario
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