Hey Felix,
records with the supplemental alignment flag are ignored when duplicate
marking is considered. They should be present in the output file, but will
not have their duplicate flag changed (or set). This is the same as
secondary alignments.
The behavior is as expected and we would be happy to accept a patch
providing the behavior you describe, but unfortunately we do not plan on
implementing this feature in the short-term.
Sincerely,
Nils Homer
On Fri, Feb 6, 2015 at 9:32 PM, Schlesinger, Felix <
fschlesin...@illumina.com> wrote:
> 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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