[BioC] Structural variations analysis

[Richard Pearson]

Hi Vincenzo

Apologies for the very delayed response! There is a function named vcf2sm in package GGtools that might help. I don't have any direct experience with 
this but thought I'd flag it up.

Best wishes

Richard

On 23/03/2011 16:14, Vincenzo Capece wrote:
> Dear all,
> i am a beginner.
> This is my first post and i hope it is clear.
> I'm developing a pipeline to analyze DNA reads from NGS machines.
> Now, after the alignemnt and the study of the SAM file,  i have a file.vcf
> and a file.snp about the structural variations of the DNA code.
> Now i want to manage those files (SAM/BAM, snp and vcf) with Bioconductor
> packages for a statistical  analysis of my variations.
> It's possible with R?
> If yes, what do you suggest?
> Thanks a lot.
> Regards,
>           V
>
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-- 
Dr Richard D Pearson                       richard.pearson at well.ox.ac.uk
Wellcome Trust Centre for Human Genetics   http://www.well.ox.ac.uk/~rpearson
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