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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