<p>I am looking at the publicly available gnomAD v3 VCF file.
The header describes the AN field as: &quot;Total number of alleles in samples.&quot;
This suggests to me that it should be a constant integer for each site.</p>
<p>However, as the example query below shows (unfortunately they removed the link to download this file, and you need to use cloud services to download the current files -&gt; <a href="https://gnomad.broadinstitute.org/downloads#v3-variants" rel="nofollow noreferrer">https://gnomad.broadinstitute.org/downloads#v3-variants</a>):</p>
<pre class="lang-bash prettyprint-override"><code>bcftools view -r chr1:15274 -H gnomad.genomes.r3.0.sites.vcf.bgz | \
awk -F[&quot;\t;&quot;] '{print $1,$2,$4,$5,$68}' -
</code></pre>
<p>This outputs (chr, pos, ref, alt, AN_afr):</p>
<pre><code>chr1 15274 A G AN_afr=19388
chr1 15274 A T AN_afr=17866
</code></pre>
<p>, i.e. the AN_afr (AN for African ancestry) is variable for the same site for two different SNVs. I've found other examples where there are three different SNVs, each with its own AN_afr. This seems to be the rule rather than the exception for multi-allelic sites, regardless of the FILTER. Can someone explain why this is?</p>
<p>I understand how it can vary between sites according to whether or not genotypes are called. What I don't understand is why it can vary at the same site? If it is indeed the case that it can vary, then what is the rule for picking a subset of samples for computing the allele frequency for one particular SNV?</p>

CC BY-SA 4.0
2020-11-25T09:44:57.980Z
It would help to have links to the data (https://storage.googleapis.com/gnomad-public/release/3.0/vcf/genomes/gnomad.genomes.r3.0.sites.vcf.bgz) and also an example of the output that you are getting. The answer here (https://github.com/broadinstitute/gnomad-browser/issues/524) suggests you are correct, but I can't actually see what you are seeing.
Maximilian Press
CC BY-SA 4.0
2020-11-25T09:51:13.787Z
See also answers https://www.biostars.org/p/360183/, https://www.biostars.org/p/329348/,
Maximilian Press
<vcf>
How does Allele Number get determined in VCF files?
# How does Allele Number get determined in VCF files?

(Asked by: username_0 on 2020-11-24)

I am looking at the publicly available gnomAD v3 VCF file.
The header describes the AN field as: "Total number of alleles in samples."
This suggests to me that it should be a constant integer for each site.
However, as the example query below shows (unfortunately they removed the link to download this file, and you need to use cloud services to download the current files -> https://gnomad.broadinstitute.org/downloads#v3-variants):
bcftools view -r chr1:15274 -H gnomad.genomes.r3.0.sites.vcf.bgz | \
awk -F["\t;"] '{print $1,$2,$4,$5,$68}' -

This outputs (chr, pos, ref, alt, AN_afr):
chr1 15274 A G AN_afr=19388
chr1 15274 A T AN_afr=17866

, i.e. the AN_afr (AN for African ancestry) is variable for the same site for two different SNVs. I've found other examples where there are three different SNVs, each with its own AN_afr. This seems to be the rule rather than the exception for multi-allelic sites, regardless of the FILTER. Can someone explain why this is?
I understand how it can vary between sites according to whether or not genotypes are called. What I don't understand is why it can vary at the same site? If it is indeed the case that it can vary, then what is the rule for picking a subset of samples for computing the allele frequency for one particular SNV?

**Tags:** vcf
> **Comments:**
> **username_1**: It would help to have links to the data (https://storage.googleapis.com/gnomad-public/release/3.0/vcf/genomes/gnomad.genomes.r3.0.sites.vcf.bgz) and also an example of the output that you are getting. The answer here (https://github.com/broadinstitute/gnomad-browser/issues/524) suggests you are correct, but I can't actually see what you are seeing.  
> **username_1**: See also answers https://www.biostars.org/p/360183/, https://www.biostars.org/p/329348/,  

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## 0 answers

