Question: Allele frequency visualization
gravatar for jaafari.omid
22 months ago by
jaafari.omid50 wrote:

Hello dears all,

Actually I have a .frq file (allele frequency file) which It is generated from .vcf file through VCFtools and it is included by five populations (The vcf file is generated by Stacks pipeline). But the point is, I don't know how can I visual the allele frequency. I will be so grateful if anyone can help me to solve this issue. Here is a part of my .frq file.

Best regards.

CM003279.1  116397  2   4   A:0.5   C:0.5
CM003279.1  184945  2   4   C:0.5   G:0.5
CM003279.1  185823  2   36  C:0.944444  T:0.0555556
CM003279.1  408595  2   54  T:0.5   A:0.5
CM003279.1  420946  2   10  A:0.5   T:0.5
CM003279.1  420946  2   42  T:0.619048  A:0.380952
CM003279.1  432468  2   4   A:0.5   T:0.5
CM003279.1  432468  2   4   T:0.5   A:0.5
CM003279.1  521247  2   6   A:0.5   C:0.5
CM003279.1  521247  2   4   C:0.5   A:0.5
CM003279.1  768668  2   46  T:0.978261  A:0.0217391
CM003279.1  768678  2   50  A:0.84  G:0.16
CM003279.1  768679  2   50  T:0.64  C:0.36
CM003279.1  768685  2   50  G:0.84  C:0.16
CM003279.1  768691  2   50  G:0.84  A:0.16
CM003279.1  768705  2   50  C:0.84  T:0.16
CM003279.1  768709  2   54  A:0.814815  T:0.185185
snp vcftools stacks R • 891 views
ADD COMMENTlink modified 20 months ago by msimmer92260 • written 22 months ago by jaafari.omid50

This question is too broad, let us know what you have in mind.

Can you share links to some papers that have the plots you liked?

ADD REPLYlink modified 22 months ago • written 22 months ago by zx87549.7k
gravatar for pltbiotech_tkarthi
20 months ago by
CIMMYT, Mexico
pltbiotech_tkarthi180 wrote:

Perhaps you can use online VEP (Variant Effector Prediction) server from ENSEMBL, just google it. I don't know whether your VCF file derived from a plant species or animal species or prokaryotic species like bacteria. Depends on the species, you can choose the correct VEP-ENSEMBL server. Here, you could predict variants effect (with SIFT score) for each position of the SNPs from your VCF input file and you have to choose the correct species of interest when you give your input VCF file. For instance, here is the VEP ENSEMBL server for plants: you can read here for variant effects prediction/variant of alleles and annotations concerning VEP server: Hope it may help.

ADD COMMENTlink modified 20 months ago • written 20 months ago by pltbiotech_tkarthi180

Sorry for the late reply.Thank you very much for giving me the direction. The species I am working is a fish.

Regards, Omid

ADD REPLYlink written 9 months ago by jaafari.omid50
gravatar for msimmer92
20 months ago by
msimmer92260 wrote:

Once I had to do that, and I made a heatmap in R. It was a good way to visualise all the SNPs' frequencies at once and see if there was one in particular that had an abnormal number (abnormal regarding your expectations, or huge difference when compared to other ones, etc). But I guess it depends on your question and the number of variants you´re handling. In my case, I had a manageable number of SNPs that I was interested in (30) and I was comparing among 5 populations, so I made 5 heatmaps with the .frq file of each.

ADD COMMENTlink modified 20 months ago • written 20 months ago by msimmer92260
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