Question: Plotting common SNPs from four individual from a vcf file
0
gravatar for vicky
18 months ago by
vicky20
Germany
vicky20 wrote:

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 • 1.1k views
ADD COMMENTlink modified 24 days ago by Biostar ♦♦ 20 • written 18 months ago by vicky20
2
gravatar for dariober
18 months ago by
dariober10k
WCIP | Glasgow | UK
dariober10k wrote:

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

ADD COMMENTlink written 18 months ago by dariober10k
0
gravatar for guillaume.rbt
18 months ago by
guillaume.rbt620
France
guillaume.rbt620 wrote:

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

ADD COMMENTlink modified 18 months ago • written 18 months ago by guillaume.rbt620
0
gravatar for geocarvalho
18 months ago by
geocarvalho110
Brazil/Recife
geocarvalho110 wrote:

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

ADD COMMENTlink written 18 months ago by geocarvalho110
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