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Question: How to perform VennDiagram from a VCF file?
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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

ADD COMMENTlink 15 months ago jaafari.omid • 40 • updated 15 months ago shubhra.bhattacharya • 120
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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 15 months ago shubhra.bhattacharya • 120
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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 15 months ago
jaafari.omid
• 40
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Can you clarify if this a multisample .vcf file i.e all the 5 samples are included in a single .vcf file?

ADD REPLYlink 15 months ago
shubhra.bhattacharya
• 120
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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 15 months ago
jaafari.omid
• 40
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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 15 months ago
jaafari.omid
• 40

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