On Thu, Feb 13, 2014 at 1:12 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> 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?
>

Thanks, Martin.

For my particular use case, simply including the insertions and deletions
covering a position in the seq and qual returned from applyPileup would be
good enough.  I don't know if there are more interesting cases that would
require more detail about the insertion or deletion, though.

Sean


>
>
>> Thanks,
>> Sean
>>
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>>
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