Question: Create a Venn diagram for 5 VCF Files (each VCF file is a population)
gravatar for mostafarafiepour
2.0 years ago by
mostafarafiepour80 wrote:

Hi All Dear,

I have 5 VCF files, each of this files is for a population. So, I want to create a Venn Diagram based on SNPs.

I have been able to find this script by searching.

vcf-compare sample1.flt.vcf.gz sample2.flt.vcf.gz > venn.out

So, How do I edit this script for my case?

Best Regard

snp venn vcf • 1.6k views
ADD COMMENTlink modified 2.0 years ago by zx87549.7k • written 2.0 years ago by mostafarafiepour80

From each VCF subset, "chrom, pos, alt, ref" columns (bcftools), read into R (or Python). Paste those columns together, then use one of the many ready packages for Venn diagrams.

ADD REPLYlink written 2.0 years ago by zx87549.7k

There is already a relevant thread in Biostars How To Create A Venn Diagram Of Sample1.Vcf, Sample2.Vcf And Sample1&2(Union).Vcf Files . Also, use upSet plots while comparing more than 3 samples together.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by Arup Ghosh2.7k
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