Thanks, all. Choice is a good thing.
Sean
On Fri, Feb 14, 2014 at 8:02 AM, Michael Lawrence wrote:
> If we're listing alternative solutions, then there's
> VariantTools::tallyVariants.
>
>
> On Fri, Feb 14, 2014 at 12:28 AM, Julian Gehring >wrote:
>
> > Hi Sean,
> >
> > You can have a look
If we're listing alternative solutions, then there's
VariantTools::tallyVariants.
On Fri, Feb 14, 2014 at 12:28 AM, Julian Gehring 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 qual
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
On Thu, Feb 13, 2014 at 1:12 PM, Martin Morgan 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 va
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 su
