How to plot venn diagram from vcf-compare output ?

Question

[sacha]

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 ?

[Benn]

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

?venn

[WouterDeCoster]

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

[sacha]

yes... but I m lazzy :D !

[Benn]

Then try venny

[WouterDeCoster]

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

[vmicrobio]

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

Answer 1

[Fae_Mah]

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

[stephane.plaisance]

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