[BioC] Structural variations analysis

[Steve Lianoglou]

Hi,

On Wed, Mar 23, 2011 at 12:14 PM, Vincenzo Capece <vivo0304 at gmail.com> 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?

Use Rsamtools to interface with your BAM files.

I have no idea what type of data you have in your *.vcf and *.snp
files, so I can't comment on that.

I think the best advice I can give you is that if you are trying to
analyze NGS data, you should get to know the IRanges, GenomicRanges,
GenomicFeatures, Biostrings, BSgenome.*, and Rsamtools  packages very
intimately.

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact