Message-ID: <52FDD394.5040601@embl.de>
Date: 2014-02-14T08:28:04Z
From: Julian Gehring
Subject: [Bioc-devel] Include indel counts in applyPileups
In-Reply-To: <CANeAVBk18aY1HNPR_BSMJPKnM1U1U-U5xNEaoS=UtFj2ZNVHxQ@mail.gmail.com>
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
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>