Re: [Vcftools-help] count the amounts of shared/specific SNPs among different groups of samples in one VCF file and SNP popularity for different number of groups

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

Hi,

one way would be to run vcf-subset to create one VCF per group, with
REF-only sites removed. Then you could use vcf-isec or vcf-compare.

Best,
Petr

On Mon, 2011-09-26 at 23:55 +0200, Mao Jianfeng wrote:
> Dear all,
> 
> I can not do lot of programming. So I would like to take more
> advantages from VCFtools or any other tools.
> 
> I would like to: 
> (1) count the amount of share/specific SNPs between any two groups of
> samples in one VCF file. 
> (2) count the amount of SNPs only occur in one group, in two groups, 3
> groups, 4 groups, ,,,,, (SNP popularity)
> I would like to know if there are any tools I can depend on? 
> 
> I checked vcf-isec and vcf-compare, it looks all these two are
> designed for count shared/specific positions, can not work on SNPs. 
> 
> As an example, I have a VCF for 30 individuals, all these 30
> individuals can be assigned to different groups (populations). Here
> may be 3 groups, each has 10 individuals. I want to count how many
> SNPs were shared/specific between group_1 and group_2, how many SNPs
> occur in 1, or 2, 3 groups, etc 
> 
> Could you please give me any directions? Thanks in advance,
> 
> Best wishes,
> 
> -- 
> Jian-Feng, Mao
> 
> Post doc
> Max Planck Institute for Developmental Biology
> Dept. of Molecular Biology
> Spemannstrasse 37-39
> 72076 Tuebingen
> Germany
> Blog: http://maojf.blogspot.com/
> 
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