Question: How to perform VennDiagram from a VCF file?
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gravatar for jaafari.omid
18 months ago by
jaafari.omid50
jaafari.omid50 wrote:

Hi all dears, I have a .VCF file which it is included by 5 populations. In this step I want to perform a VennDiagram but I don't know how can I do it? Actually what should be the input file to do it? should I use my .vcf file?

Any solution and suggestion would be appreciated in advance.

Cheers

snp venndiagram genome • 637 views
ADD COMMENTlink modified 18 months ago by shubhra.bhattacharya120 • written 18 months ago by jaafari.omid50
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gravatar for shubhra.bhattacharya
18 months ago by
shubhra.bhattacharya120 wrote:

Hey! You can use venny or jvenn online if the file is not too big. The input can be chromosome and position from your .vcf file which are the first two columns. You can paste them with a delimiter to get a unique key for each entry.

http://bioinfogp.cnb.csic.es/tools/venny/
http://jvenn.toulouse.inra.fr/app/example.html

You can use R if you're familar with it.

https://stats.idre.ucla.edu/r/faq/how-can-i-generate-a-venn-diagram-in-r/
ADD COMMENTlink written 18 months ago by shubhra.bhattacharya120

Thank you so much for your answer. Sorry maybe I couldn't completely catch what exactly you have mentioned. You mean I should generate an input file including all possible combinations between my populations in two columns (Chromosome and position)? So there is no needing to have a third column as SNP or Fst?

Cheers,

ADD REPLYlink written 18 months ago by jaafari.omid50

Can you clarify if this a multisample .vcf file i.e all the 5 samples are included in a single .vcf file?

ADD REPLYlink written 18 months ago by shubhra.bhattacharya120

Yes it is just a single .vcf file which is included by 130 samples and these 130 samples belong to 5 different groups or locations. So there is just one .vcf file.

ADD REPLYlink written 18 months ago by jaafari.omid50

okay got it! Did you find this link relevant- How To Create A Venn Diagram Of Sample1.Vcf, Sample2.Vcf And Sample1&2(Union).Vcf Files

ADD REPLYlink written 18 months ago by shubhra.bhattacharya120

Yes I have seen it already but if I've understood it correctly, it is for comparison between for example 3 .vcf files but for me it is just one .vcf file.

ADD REPLYlink written 18 months ago by jaafari.omid50
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