On Mon, Dec 6, 2010 at 9:40 AM, Vincent Carey <stvjc@channing.harvard.edu>wrote:

> On Mon, Dec 6, 2010 at 11:28 AM, Sean Davis <sdavis2@mail.nih.gov> wrote:
> > On Mon, Dec 6, 2010 at 9:54 AM, Mao Jianfeng <jianfeng.mao@gmail.com>
> wrote:
> >
> >> Dear Bioconductor listers,
> >>
> >> I am new to genomics and bioinformatics. In my current study, we have
> >> sequenced the genomes of tens of accessions of a plant, using Illumina
> >> next generation sequencer. The short reads of a specific accession
> >> have been aligned to the reference. The SNPs and shor indels have been
> >> predicted for a specific accession genome to the reference. we got the
> >> data sets for SNPs like the following format (in text file, the column
> >> names were listed, the accession name will not change for a specific
> >> accession):
> >>
> >> <accession name><chromosome><position><reference base><cons
> >> base><quality><support><concordance><avg_hits>
> >>
> >>
> >> But usually, we need to align all the accessions in the following
> >> format for classical population genetic analysis:
> >>
> >> <accessions><SNP_1><SNP_2><SNP_3><SNP_...>
> >> accession_1, a,t,g,,,
> >> accession_2, a,t,c,,,
> >> accession_3, t,a,c,,,
> >> accession_,,,,,,,,,,,,,
> >>
> >> I need to get helps, suggestions on how to do this format conversion,
> >> or if there are any alternative choices for me, by using R and
> >> bioconductor? If it need database operations, and how to do that?
> >>
> >> Thanks in advance.
> >>
> >>
> >
> > Hi, Jianfeng.  You might save yourself some trouble by using a format
> such
> > as VCF, something that is approaching an standard for reporting and
> > databasing variants.  If you write a script to convert your variant
> format
> > to a VCF, then combining them can be done with vcftools or potentially
> other
> > tools dealing with VCF.
>
> I will add here that there is very rudimentary code for transforming VCF to
> SnpMatrix instances in the devel branch of GGtools: called vcf2sm
>
> The intention is to speed the path from variant representations for
> multiple subjects as given in the
> 1000 genomes files to structures analyzable with the snpMatrix2
> facilities.  However, the specific
> implementation in vcf2sm requires that system("tabix") works.
> Rsamtools facilities for working
> with bcf are also relevant but have not been connected to the
> SnpMatrix representation yet.
>
>
The snpMatrix(2) package looks interesting. It would be great if it were
better integrated with IRanges/GenomicRanges. For example, the snp.support
object could be a RangedData or GRanges.

>
> > Sean
> >
> >        [[alternative HTML version deleted]]
> >
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