[Bioc-devel] Include indel counts in applyPileups

[Martin Morgan]

On 02/13/2014 08:09 AM, Sean Davis wrote:
> Hi, Martin.
>
> How difficult would it be to include insertions/deletions in seq and qual
> in the applyPileups method for PileupFiles?  The use case is to look at the
> context around variants for increases mismatch rates.  Indels will have a
> small impact on such calculations, but for completeness it would be nice to
> have.

Actually we're in the process of revisiting how pileups are calculated, so it's 
a great time to express what you'd like. Are you asking for per-position 
information on indel occurrence? Martin

>
> Thanks,
> Sean
>
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>
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