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<div>A follow-up:<br>
</div>
<div><br>
</div>
<div>I am also seeing oddly parsed frequencies for 'gnomAD' see below.</div>
<div><br>
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<div>I am using VEP version 95.1 <br>
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<div><br>
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<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>
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<div><br>
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<span></span><br>
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<div><br>
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<div><br>
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<div>________________________________________<br>
</div>
<div>From: Joseph A Prinz<br>
</div>
<div>Sent: Thursday, February 28, 2019 12:42 PM<br>
</div>
<div>To: dev@ensembl.org<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>
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<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>
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<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>
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<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>
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<div><br>
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<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>
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