Question: How to plot venn diagram from vcf-compare output ?
0
gravatar for sacha
3.3 years ago by
sacha2.0k
France
sacha2.0k wrote:

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 ?

plot vcf-compare venn • 2.5k views
ADD COMMENTlink modified 2 days ago by Fae_Mah0 • written 3.3 years ago by sacha2.0k

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

?venn
ADD REPLYlink written 3.3 years ago by Benn8.0k

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

ADD REPLYlink written 3.3 years ago by WouterDeCoster44k

yes... but I m lazzy :D !

ADD REPLYlink written 3.3 years ago by sacha2.0k

Then try venny

ADD REPLYlink written 3.3 years ago by Benn8.0k

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

ADD REPLYlink written 3.3 years ago by WouterDeCoster44k

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

ADD REPLYlink written 3.3 years ago by vmicrobio250
0
gravatar for Fae_Mah
2 days ago by
Fae_Mah0
Fae_Mah0 wrote:

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

ADD COMMENTlink modified 2 days ago • written 2 days ago by Fae_Mah0
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