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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Dr Richard D Pearson richard.pearson at well.ox.ac.uk Wellcome Trust Centre for Human Genetics http://www.well.ox.ac.uk/~rpearson University of Oxford Tel: +44 (0)1865 617890 Roosevelt Drive Mob: +44 (0)7971 221181 Oxford OX3 7BN, UK Fax: +44 (0)1865 287664

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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > Dr Richard D Pearson ? ? ? ? ? ? ? ? ? ? ? richard.pearson at well.ox.ac.uk > Wellcome Trust Centre for Human Genetics > http://www.well.ox.ac.uk/~rpearson > University of Oxford ? ? ? ? ? ? ? ? ? ? ? Tel: +44 (0)1865 617890 > Roosevelt Drive ? ? ? ? ? ? ? ? ? ? ? ? ? ?Mob: +44 (0)7971 221181 > Oxford OX3 7BN, UK ? ? ? ? ? ? ? ? ? ? ? ? Fax: +44 (0)1865 287664 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >