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

[Petr D. <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.

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.
> 
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