On 17 Sep 2014, at 20:53, Ni Huang <[email protected]> wrote:
> in this BAM, the primary and the supplementary alignment of each read are
> mis-labeled as a read pair (the 7th and 8th column). I had a samtools fixmate
> (version 0.1.19) step before Picard Markduplicates, which might be the real
> culprit, as the error from MarkDuplicates disappeared after I removed the
> fixmate step.
Samtools 0.1.19 predated the introduction of supplementary reads by a couple of
months, and so unsurprisingly its fixmate command did not handle them correctly
and could lead to this sort of problem.
Fixmate in version 1.0 doesn't handle supplementary reads properly either [1],
and there is a fairly imminent 1.1 release that will include this fix.
John
[1] Subsequently fixed by
https://github.com/samtools/samtools/commit/57e71e72d3638d3505dae1bd6c4d921fb98c8c5d
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