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

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

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.