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

[Mao J. <jia...@gm...>]

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.
>>
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>
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