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.

Sean

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