[BioC] Structural variations analysis

[Vincent Carey]

Thanks for mentioning this Richard.  The GGtools vcf2sm has a limited
use case at present -- translating calls published by the 1000 genomes
project to snpStats SnpMatrix instances.  Only the genotype call
values are used; information on call uncertainty is not yet propagated
by vcf2sm.

The samtools suite includes bcftools.  As I understand it, samtools
mpileup will generate vcf or bcf and such files can be imported or
scanned using Rsamtools scanBcf.  Last time I checked, bcftools did
not work with 1000 genomes-generated VCF.

On Tue, Apr 5, 2011 at 6:44 AM, Richard Pearson
<richard.pearson at well.ox.ac.uk> wrote:
> 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
>>
>>        [[alternative HTML version deleted]]
>>
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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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