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<p>Dear Beat,</p>
<p>We have some documentation in the Ensembl Glossary [<a
moz-do-not-send="true"
href="https://www.ensembl.org/Multi/Help/Glossary?db=core">https://www.ensembl.org/Multi/Help/Glossary?db=core</a>]
(not that easy to find):</p>
<b>- Global MAF (Global Minor Allele Frequency):</b><br>
Minor Allele Frequency (MAF) refers to the frequency of the second
most common allele at the position where a sequence variant (such as
a SNP) has been identified. In Ensembl, the global MAF is calculated
using the allele frequencies across all 1000 Genomes Phase 3
populations.<br>
<br>
We also display the "Highest population MAF", which corresponds to
the highest MAF found in the main human genotyping projects we have
in Ensembl (<a moz-do-not-send="true"
href="http://www.ensembl.org/info/genome/variation/data_description.html#populations">http://www.ensembl.org/info/genome/variation/data_description.html#populations</a>).
<p><font face="Helvetica, Arial, sans-serif">In the Ensembl REST VEP
endpoint, this 1000 Genomes MAF correspond to the
"minor_allele_freq" information.</font></p>
<p><font face="Helvetica, Arial, sans-serif">Th<code><font
face="Helvetica, Arial, sans-serif">e "gnomad<font
face="Helvetica, Arial, sans-serif">_maf" is calcula<font
face="Helvetica, Arial, sans-serif">ted from the <font
face="Helvetica, Arial, sans-serif">g<font
face="Helvetica, Arial, sans-serif">nomA<font
face="Helvetica, Arial, sans-serif">D VCF files
(which provides allele count<font face="Helvetica,
Arial, sans-serif">s</font> and frequencies).</font></font></font></font></font></font></code></font></p>
<p><font face="Helvetica, Arial, sans-serif"><code><font
face="Helvetica, Arial, sans-serif"><font face="Helvetica,
Arial, sans-serif"><font face="Helvetica, Arial,
sans-serif"><font face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"><br>
</font></font></font></font></font></font></code></font></p>
<p><font face="Helvetica, Arial, sans-serif"><code><font
face="Helvetica, Arial, sans-serif"><font face="Helvetica,
Arial, sans-serif"><font face="Helvetica, Arial,
sans-serif"><font face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif">We will tr<font
face="Helvetica, Arial, sans-serif">y to <font
face="Helvetica, Arial, sans-serif">improve
our do<font face="Helvetica, Arial,
sans-serif">cum<font face="Helvetica,
Arial, sans-serif">entation about the
MAF in the next Ensembl release.</font></font></font></font></font></font></font></font></font></font></font></font></code></font></p>
<p><font face="Helvetica, Arial, sans-serif"><code><font
face="Helvetica, Arial, sans-serif"><font face="Helvetica,
Arial, sans-serif"><font face="Helvetica, Arial,
sans-serif"><font face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"><code><font
face="Helvetica, Arial,
sans-serif"><font
face="Helvetica, Arial,
sans-serif"><font
face="Helvetica, Arial,
sans-serif"><font
face="Helvetica, Arial,
sans-serif"><font
face="Helvetica, Arial,
sans-serif"><font
face="Helvetica,
Arial, sans-serif">I h<font
face="Helvetica,
Arial, sans-serif">ope
<font
face="Helvetica,
Arial, sans-serif">this
helps.</font></font></font></font></font></font></font></font></code></font></font></font></font></font></font></font></font></font></font></font></font></font></code></font></p>
<p><font face="Helvetica, Arial, sans-serif"><code><font
face="Helvetica, Arial, sans-serif"><font face="Helvetica,
Arial, sans-serif"><font face="Helvetica, Arial,
sans-serif"><font face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif">Best regards,<br>
</font></font></font></font></font></font></code></font></p>
<p><font face="Helvetica, Arial, sans-serif"><code><font
face="Helvetica, Arial, sans-serif"><font face="Helvetica,
Arial, sans-serif"><font face="Helvetica, Arial,
sans-serif"><font face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"><font
face="Helvetica, Arial, sans-serif"></font></font></font></font></font></font></code>
<code class="json"><span class="hljs-value"><span
class="hljs-attribute"></span></span></code></font></p>
<pre class="moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
<div class="moz-cite-prefix">On 29/01/2018 16:16, Wolf Beat wrote:<br>
</div>
<blockquote type="cite"
cite="mid:fa75b6b16a81412d9875a33e363ad3c6@hefr.ch">
<pre wrap="">Hello,
i have a question that i sadly could not find an answer in the documentation (but its likely somewhere, i just can't find it).
For human variants there is a MAF number displayed on the website. It is usually written in a tooltip where this information comes from. But, if there are multiple MAF sources, how is the MAF choosen?
I guess this question also applies to the VEP rest service, which sometimes (not always!) returns a "minor_allele_freq" information. From what i understand, thats the same as the one displayed on the website, but again, how is it calculated?
I know that VEP also provides me with gnomad_maf etc. But that "Global" MAF Number is calculated how exactly?
I'm sure this is documented somewhere, but i must have choosen the wrong keywords. Thank you for pointing me towards the correct information!
Kind regards
Beat Wolf
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</pre>
</blockquote>
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