Allele frequency calculation
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2.6 years ago
rheab1230 ▴ 140

Hello everyone, I use vcf tools to find AF values by using this command:

vcftools --gzvcf $SUBSET_VCF --freq2 --out $OUT --max-alleles 2

The output I got from this is:

chr      pos nalleles  nchr    a1     a2    
  <dbl>    <dbl>    <dbl> <dbl> <dbl>  <dbl>  
1    22 16050408        2   846 0.944 0.0556 
2    22 16050612        2   846 0.937 0.0626 
3    22 16050678        2   846 0.948 0.0520 
4    22 16050984        2   846 1     0      
5    22 16051107        2   846 0.943 0.0567 
6    22 16051249        2   846 0.927 0.0733 

Now I know in order to find minor allele frequency (MAF): i use this command: find minor allele frequency

var_freq$maf <- var_freq %>% select(a1, a2) %>% apply(1, function(z) min(z))

But I need to plot total allele frequency and not MAF. Should i consider both a1 and a2 value for plotting?

AF VCF snp calc • 1.6k views
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"Total allele frequency" will always be 1. Do you want to plot the frequency of just the ALT allele, just the minor allele, or of all alleles?

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I have plotted one for minor allele. My supervisor told me to plot allele frequency distribution for the vcf files. He didn't mentioned anything specific.

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Your question should be addressed to your supervisor, then - it does not belong on a public forum.

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I will contact my supervisor regarding this. Suppose I want to plot ALT allele frequency, how should I do that?

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Understand which column contains the data you need, how you need to plot it and then build the code that generates that plot. You will need to do a whole bunch of google searches.

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2.6 years ago
sbstevenlee ▴ 480

If you don't mind Python API, have a look at the pyvcf.VcfFrame.plot_region method I wrote:

Below is a simple example:

from fuc import pyvcf, common
import matplotlib.pyplot as plt
common.load_dataset('pyvcf')
vcf_file = '~/fuc-data/pyvcf/getrm-cyp2d6-vdr.vcf'
vf = pyvcf.VcfFrame.from_file(vcf_file)
vf.plot_region('NA18973')
plt.tight_layout()

enter image description here

We can display allele fraction of REF and ALT instead of DP:

ax = vf.plot_region('NA18973', k='#AD_FRAC_REF', label='REF')
vf.plot_region('NA18973', k='#AD_FRAC_ALT', label='ALT', ax=ax)
plt.tight_layout()

enter image description here

Note that the method is only available in the 0.21.0-dev version of the fuc package. If you need help installing this development version, please let me know in the comment.

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