When I checked the source code, I found that bwa actually reports
alternative mapped quality in "AM" tag. Note that the "Aq" tag in the
G1K alignment is actually a bug. There is no Aq defined in the
specification in fact. It should be AM.
Heng
On Tue, Jul 21, 2009 at 02:01:41PM -0500, Ken Chen wrote:
> Hello Heng,
>
> I am investigating the performance of BWA-based SV detection. Does
> BWA track alternative mapping quality? Can there be a BWA specific
> flag in SAM for alternative mapping quality? I think it is still
> useful. In my evaluation, alternative mapping quality consistently
> produces better results than the (joint) mapping quality or single-
> end mapping quality.
>
> -Ken
>
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