Allele frequency visualization

Question

[jaafari.omid]

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.

CHROM   POS N_ALLELES   N_CHR   {ALLELE:FREQ}
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

[zx8754]

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?

Answer 1

[pltbiotech_tkarthi]

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: https://plants.ensembl.org/Triticum_aestivum/Tools/VEP?db=core you can read here for variant effects prediction/variant of alleles and annotations concerning VEP server: https://plants.ensembl.org/Help/View?id=484 Hope it may help.

[jaafari.omid]

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

Regards, Omid

Answer 2

[msimmer92]

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.

[Ivvyray_genomics]

I have 110 samples in a multi-sample vcf file and generated a .frq file (allele frequency file) using vcftools. I have tried to plot af density using the plot(density) in R but it keeps giving error as it gets stuck (argument 'X' must be numeric). Please how did you plot your heat maps? If you can share your script that would be great. Many thanks