Hi,
I could not find any documentation on this: How is MarkDuplicates supposed to
interact with supplemental alignments (flag 2048)? At the moment (1.128) it
seems these alignments are never marked as duplicates, even if the
corresponding primary alignments are marked. Is that the intended behavior (or
am I doing something wrong)? Intuitively it would seem to me that 'isDuplicate'
is a property of the fragment, not just the primary alignment. Otherwise there
is no way to tell if two supplemental alignments are independent evidence for
e.g. a translocation event without jumping in the bam file to the position of
the primary.
Thank you
Felix Schlesinger
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