Plotting common SNPs from four individual from a vcf file
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6.2 years ago
vicky ▴ 30

Hi

I have got the vcf file with the SNP informations from four individuals. I want to make a Venn diagram (or another graphical display of the SNPs) of the SNPs? To see how many SNPs are shared and private between these four individuals. Is there a tool who does it. My data looks like this :

##fileformat=VCFv4.1
##contig=<ID=1,length=48143371>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Indi_A   Indi_B   Indi_C  Indi_D
1       50      .       G       C       .       .       .       GT      0       0       0       1
1       55      .       G       T       .       .       .       GT      0       1       0       1
1       267     .       G       T       .       .       .       GT      0       0       1       0
1       271     .       T       G       .       .       .       GT      0       1       0       0
1       366     .       C       A       .       .       .       GT      0       1       0       0

Thanks

SNP • 2.9k views
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Entering edit mode
6.2 years ago

Once again, I'm going to suggest UpSetR. A venn diagram with four intersections starts being quite messy.

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6.2 years ago
guillaume.rbt ★ 1.0k

I dont't know a tool that does that directly.

But you can extract the SNPs that intersects between your individuals manually and then do Venn diagrams.

You can do that with SNPSift for example.

see : Filter genotype in multi-sample VCF file

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6.2 years ago
geocarvalho ▴ 360

http://bioinformatics.psb.ugent.be/webtools/Venn/ I normally use it

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