[Bioc-devel] Include indel counts in applyPileups

[Julian Gehring]

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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