If we're listing alternative solutions, then there's
VariantTools::tallyVariants.


On Fri, Feb 14, 2014 at 12:28 AM, Julian Gehring <julian.gehring@embl.de>wrote:

> Hi Sean,
>
> You can have a look at the 'bam2R' function from the 'deepSNV' package.
>  This will extract the base/insertion/deletion counts, base call qualities,
> and other metrics strand-specific from a BAM file.
>
> Best wishes
> Julian
>
>
>
> On 13/02/14 17:09, 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.
>>
>> Thanks,
>> Sean
>>
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>>
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