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<p>Dear Joseph,<br>
<br>
Thank you for reporting this.</p>
<p><br>
</p>
<p>By default/design the JSON output only displays in "frequency"
the frequencies related to the alternative allele(s) you used in
your input file, e.g. :</p>
<p><br>
</p>
<p># Your input: <br>
</p>
<p> 14:105415607 C/<b>G</b><br>
</p>
<p># Your output:</p>
<p> "AA": "T:0",<br>
"EA": "T:0.0006983",</p>
<p> "frequencies": {<br>
</p>
<div> "<b>G</b>": {<br>
</div>
<div> "afr": "0.0015",<br>
</div>
<div> "amr": "0",<br>
</div>
<div> "eas": "0.001",<br>
</div>
<div> "eur": "0",<br>
</div>
<p>
"gnomad": "0.0002357",</p>
<p> ...}</p>
<p> },</p>
<p> "allele_string": "C/A/<b>G</b>/T",</p>
<p> "id":"rs112699389"<br>
</p>
<p><br>
</p>
<p>However it also returns the corresponding minor allele frequency
for ESP populations in a separate part of the JSON if the
alternative differs from your alternative allele. In the example
above, the alternative allele for rs112699389 in the ESP
populations is T.<br>
</p>
<p><br>
</p>
<p><br>
For the second issue, it looks like you are using the flag "<a
moz-do-not-send="true"
href="https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_no_check_alleles">--no_check_alleles</a>".
This flag doesn't compare which is/are your input alternative
allele(s) with the co-located alleles and simply list the
frequencies of each alternative allele of the co-located variants,
e.g.:<br>
</p>
<p><br>
</p>
<p># Input: <br>
</p>
<p> 2:36785668 A/T<br>
</p>
<p># Output:</p>
<p> "AA":"<b>AA</b>:0.01702,-:0.02651",<br>
"EA":"<b>AA</b>:0.01386,<b>-</b>:0.02891",<br>
"gnomAD_SAS":"<b>-</b>:0.1864,<b>AA</b>:0.08409",<br>
"gnomAD_OTH":"<b>-</b>:0.1465,<b>AA</b>:0.05941",<br>
"gnomAD_EAS":"<b>-</b>:0.1653,<b>AA</b>:0.08157",<br>
"gnomAD_ASJ":"<b>-</b>:0.1746,<b>AA</b>:0.05098",<br>
"gnomAD_AMR":"<b>-</b>:0.1808,<b>AA</b>:0.08017",<br>
"gnomAD":"<b>-</b>:0.1349,<b>AA</b>:0.05111",<br>
"gnomAD_NFE":"<b>-</b>:0.1172,<b>AA</b>:0.03693",<br>
"gnomAD_FIN":"<b>-</b>:0.09683,<b>AA</b>:0.029",<br>
"allele_string":"A/<b>AA</b>/<b>-</b>",<br>
</p>
<p> "id":"TMP_ESP_2_36785668_36785668",</p>
<p><br>
<br>
I agree that these different ways to display the frequencies of
the co-located variants can be confusing and we will try to make
it easier to read/parse.<br>
</p>
<p><br>
</p>
<p>Best regards,<br>
</p>
<pre class="moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
<div class="moz-cite-prefix">On 28/02/2019 20:28, Joseph A Prinz
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:SN6PR05MB5470427917BF299BB9F53DD2E5750@SN6PR05MB5470.namprd05.prod.outlook.com">
<meta http-equiv="Content-Type" content="text/html;
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<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
<div>A follow-up:<br>
</div>
<div><br>
</div>
<div>I am also seeing oddly parsed frequencies for 'gnomAD' see
below.</div>
<div><br>
</div>
<div>I am using VEP version 95.1 <br>
</div>
<div><br>
</div>
<div>Thanks again,</div>
<div>Joey<br>
</div>
<div><br>
</div>
<div><span>'colocated_variants': [<br>
</span>
<div>{ 'AA': '-:0.02651',<br>
</div>
<div> 'EA': '-:0.02891',<br>
</div>
<div> 'allele_string': 'A/-',<br>
</div>
<div> 'end': '36785668',<br>
</div>
<div> 'gnomAD': '-:0.1349',<br>
</div>
<div> 'gnomAD_AFR': '-:0.104',<br>
</div>
<div> 'gnomAD_AMR': '-:0.1808',<br>
</div>
<div> 'gnomAD_ASJ': '-:0.1746',<br>
</div>
<div> 'gnomAD_EAS': '-:0.1653',<br>
</div>
<div> 'gnomAD_FIN': '-:0.09683',<br>
</div>
<div> 'gnomAD_NFE': '-:0.1172',<br>
</div>
<div> 'gnomAD_OTH': '-:0.1465',<br>
</div>
<div> 'gnomAD_SAS': '-:0.1864',<br>
</div>
<div> 'id': 'rs756392461',<br>
</div>
<div> 'start': '36785668',<br>
</div>
<div> 'strand': '1'},<br>
</div>
<div>{ 'AA': 'AA:0.01702,-:0.02651',<br>
</div>
<div> 'EA': 'AA:0.01386,-:0.02891',<br>
</div>
<div> 'allele_string': 'A/AA/-',<br>
</div>
<div> 'end': '36785668',<br>
</div>
<div> 'gnomAD': '-:0.1349,AA:0.05111',<br>
</div>
<div> 'gnomAD_AFR': '-:0.104,AA:0.05793',<br>
</div>
<div> 'gnomAD_AMR': '-:0.1808,AA:0.08017',<br>
</div>
<div> 'gnomAD_ASJ': '-:0.1746,AA:0.05098',<br>
</div>
<div> 'gnomAD_EAS': '-:0.1653,AA:0.08157',<br>
</div>
<div> 'gnomAD_FIN': '-:0.09683,AA:0.029',<br>
</div>
<div> 'gnomAD_NFE': '-:0.1172,AA:0.03693',<br>
</div>
<div> 'gnomAD_OTH': '-:0.1465,AA:0.05941',<br>
</div>
<div> 'gnomAD_SAS': '-:0.1864,AA:0.08409',<br>
</div>
<div> 'id': 'TMP_ESP_2_36785668_36785668',<br>
</div>
<div> 'start': '36785668',<br>
</div>
<div> 'strand': '1'}<br>
</div>
<div>]<br>
</div>
<div><br>
</div>
<span></span><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>________________________________________<br>
</div>
<div>From: Joseph A Prinz<br>
</div>
<div>Sent: Thursday, February 28, 2019 12:42 PM<br>
</div>
<div>To: <a class="moz-txt-link-abbreviated" href="mailto:dev@ensembl.org">dev@ensembl.org</a><br>
</div>
<div>Subject: Quick question about --af_esp option in VEP<br>
</div>
<div><br>
</div>
<div>Hi VEP devs,<br>
</div>
<div><br>
</div>
<div>I wanted to confirm the output of --af_esp when using JSON
output.<br>
</div>
<div><br>
</div>
<div>Some times I see values represented 'aa' and 'ea' nested
under 'frequencies', and sometimes I see values "AA" and "EA"
not nested under 'frequencies'.<br>
</div>
<div>Further when appearing as "AA" / "EA" the values do not seem
to be parsed in the same way (they appear as
"allele:frequency").<br>
</div>
<div><br>
</div>
<div>I am not sure which values to use, and neither are keyed as
'aa_af' or 'ea_af' as I would expect from the documentation.<br>
</div>
<div><br>
</div>
<div>Below are examples of both scenarios.<br>
</div>
<div><br>
</div>
<div>Thanks for taking a look!<br>
</div>
<div>Joey<br>
</div>
<div><br>
</div>
<div>"colocated_variants": [<br>
</div>
<div> {<br>
</div>
<div> "allele_string": "A/G/T",<br>
</div>
<div> "end": "69511",<br>
</div>
<div> "frequencies": {<br>
</div>
<div> "G": {<br>
</div>
<div> "aa": "0.5441",<br>
</div>
<div> "ea": "0.8874",<br>
</div>
<div> "gnomad": "0.9506",<br>
</div>
<div> "gnomad_afr": "0.6074",<br>
</div>
<div> "gnomad_amr": "0.9508",<br>
</div>
<div> "gnomad_asj": "0.9779",<br>
</div>
<div> "gnomad_eas": "0.9995",<br>
</div>
<div> "gnomad_fin": "0.9915",<br>
</div>
<div> "gnomad_nfe": "0.9728",<br>
</div>
<div> "gnomad_oth": "0.9499",<br>
</div>
<div> "gnomad_sas": "0.9854"<br>
</div>
<div> }<br>
</div>
<div> },<br>
</div>
<div> "id": "rs2691305",<br>
</div>
<div> "start": "69511",<br>
</div>
<div> "strand": "1"<br>
</div>
<div> }<br>
</div>
<div>]<br>
</div>
<div><br>
</div>
<div>"colocated_variants": [<br>
</div>
<div> {<br>
</div>
<div> "AA": "T:0",<br>
</div>
<div> "EA": "T:0.0006983",<br>
</div>
<div> "allele_string": "C/A/G/T",<br>
</div>
<div> "end": "105415607",<br>
</div>
<div> "frequencies": {<br>
</div>
<div> "G": {<br>
</div>
<div> "afr": "0.0015",<br>
</div>
<div> "amr": "0",<br>
</div>
<div> "eas": "0.001",<br>
</div>
<div> "eur": "0",<br>
</div>
<div> "gnomad": "0.0002357",<br>
</div>
<div> "gnomad_afr": "0.0002741",<br>
</div>
<div> "gnomad_amr": "0.0005474",<br>
</div>
<div> "gnomad_asj": "0",<br>
</div>
<div> "gnomad_eas": "0.0004838",<br>
</div>
<div> "gnomad_fin": "0",<br>
</div>
<div> "gnomad_nfe": "1.384e-05",<br>
</div>
<div> "gnomad_oth": "0",<br>
</div>
<div> "gnomad_sas": "0.0006331",<br>
</div>
<div> "sas": "0.0133"<br>
</div>
<div> }<br>
</div>
<div> },<br>
</div>
<div> "id": "rs112699389",<br>
</div>
<div> "minor_allele": "T",<br>
</div>
<div> "minor_allele_freq": "0.0072",<br>
</div>
<div> "start": "105415607",<br>
</div>
<div> "strand": "1"<br>
</div>
<div> }<br>
</div>
<div>]<br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
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