On Mon, Dec 6, 2010 at 11:35 AM, Mao Jianfeng <jianfeng.mao@gmail.com>wrote: > Dear Mr/Ms. Sean, > > Thanks a lot. > > 1. for VCF, I found: > http://genome.sph.umich.edu/wiki/VcfCodingSnps > > 2. an other question: > If what VCF do is like mpileup in samtools or Multi-sample SNP calling > in GATK v2. > > samtoosl: > http://samtools.sourceforge.net/mpileup.shtml > > GATK: > http://www.broadinstitute.org/gsa/wiki/index.php > > I just got this idea. > > Jian-feng > Hi, Jien-feng. VCF is a file format. It does not "do" anything. While other formats include the same information, using a standard format such as VCF gives you access to third-party tools for doing things like combining, subsetting, etc. I should have included a link to the format spec: http://www.1000genomes.org/wiki/Analysis/variant-call-format Yes, samtools mpileup and GATK unified genotyper are a couple of tools that generate VCF. Sean 2010/12/6 Sean Davis <sdavis2@mail.nih.gov>: > > > > > > 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 > > > > > > -- > Jian-Feng, Mao > > the Institute of Botany, > Chinese Academy of Botany, > [[alternative HTML version deleted]]