Re: [Vcftools-help] calculate the frequency distribution of different types of variations in accessions and populations

[Petr D. <pd...@sa...>]

Hi Mao,

please take a look at the VCF specification, both tags are described
there
http://vcftools.sourceforge.net/specs.html

Best,
Petr



On Thu, 2011-04-07 at 17:37 +0200, Mao Jianfeng wrote:
> Dear Petr,
> 
> Thanks a lot for your kind reply.
> 
> I will try them out. But, please see the followings.
> 
> 
> 2011/4/7 Petr Danecek <pd...@sa...>:
> > Hi Mao,
> >
> > if you want to use existing tools, the script fill-an-ac can calculate
> > the value of AN and AC tags. Then you could get the stats using
> > vcf-stats -f INFO/AN,INFO/AC.
> 
> I have no idea about AN and AC tags. I have not find enough INFO about
> them. I want to understand them more. Could you please give me more
> explanation on them, or point out where I can find them in detail?
> 
> I am new to genomics, and I have no colleagues who use VCF and
> VCFTools tool. So my improvement depends on the mailing list.
> 
> Thanks in advance.
> 
> >
> > For the second task I'd create one VCF file per population using
> > vcf-subset and then vcf-compare to get the numbers you want.
> >
> > Hope this helps,
> > Petr
> >
> >
> > On Thu, 2011-04-07 at 11:42 +0200, Mao Jianfeng wrote:
> >> Dear vcftools-listers,
> >>
> >> VCF format and VCFTOOLS eased my work of NGS genomics. Thanks a lot
> >> for its generation.
> >>
> >> I am facing problem, when I attempt to calculate the frequency
> >> distribution of different types of variations in accessions and
> >> populations. I am new to genomics and not good at computer. I would
> >> like to hear advice/directions from you.
> >>
> >> I have NGS genomic data from 100 individuals of 10 geographic regions.
> >> The data (snp, indels) have been in VCF format. Now, I asked two
> >> problems.
> >>
> >> (1) what is the frequency distribution of genomic variants (snp,
> >> indel) in the different numbers of individuals? For example, in my
> >> case, I want to count how many snp/indel occurred in 10 individuals,
> >> 20 individuals, 30, 40 ,50 ,60, 70, 80, 90, 100 (the whole data).
> >>
> >> (2) what is the frequency distribution of genomic variants (snp,
> >> indel) in the different numbers of populations? For example, in my
> >> case, I want to count how many snp/indel occurred in 2 populations, 4
> >> populations, 6, 8, 10 (the whole data).
> >>
> >> I check the manu for VCFTOOLS, but I have not find functionality for
> >> these two jobs. Have you, any listers, faced the same problems? What
> >> is your strategy for that? Could you please share any hints with me?
> >> And, I think you advice should be valuable for all the VCF users.
> >>
> >> Thanks a lot in advance.
> >>
> >> ------------------------------------------------------------------------------
> >> Xperia(TM) PLAY
> >> It's a major breakthrough. An authentic gaming
> >> smartphone on the nation's most reliable network.
> >> And it wants your games.
> >> http://p.sf.net/sfu/verizon-sfdev
> >> _______________________________________________
> >> Vcftools-help mailing list
> >> Vcf...@li...
> >> https://lists.sourceforge.net/lists/listinfo/vcftools-help
> >
> >
> >
> >
> > --
> >  The Wellcome Trust Sanger Institute is operated by Genome Research
> >  Limited, a charity registered in England with number 1021457 and a
> >  company registered in England with number 2742969, whose registered
> >  office is 215 Euston Road, London, NW1 2BE.
> >




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.