How to plot venn diagram from vcf-compare output ?

i get the following output from vcf-compare by comparing two VCF :

VN      2172    NA12878/intersect2.vcf.gz (6.8%)
VN      29648   Coriell.varscan.snp.vcf.gz (20.7%)      NA12878/intersect2.vcf.gz (93.2%)
VN      113680  Coriell.varscan.snp.vcf.gz (79.3%)

I would like to plot a Venn diagram quickly. Any idea ? Online tool ? R tool ? command line tool ?

vcf-compare venn plot

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updated 3.3 years ago by stephane.plaisance •

• written 9.1 years ago by sacha

The gplots lib in R contains a venn() function.

?venn

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written 9.1 years ago by Benn

I guess you could easily write an Rscript using the VennDiagram package for this purpose.

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written 9.1 years ago by WouterDeCoster

yes... but I m lazzy :D !

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written 9.1 years ago by sacha

Then try venny

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written 9.1 years ago by Benn

Same. Googling "online venn diagram" also brings up some hits :)

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written 9.1 years ago by WouterDeCoster

several resources : http://research.stowers.org/mcm/venn.html

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written 9.1 years ago by vmicrobio

1 answer

you can use 2DVenn.R , see these links https://wiki.bits.vib.be/index.php/NGS_Exercise.6#compare_aln_.26_mem_results_with_vcf-compare https://wiki.bits.vib.be/index.php/Create_Venn_plots_from_counts

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written 5.8 years ago by Fae_Mah •

https://github.com/BITS-VIB/venn-tools

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written 3.3 years ago by stephane.plaisance •

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