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<div>Hi VEP devs,<br>
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<div>I wanted to confirm the output of --af_esp when using JSON output.</div>
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<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'.</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").</div>
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<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.</div>
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<div>Below are examples of both scenarios.</div>
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<div>Thanks for taking a look!</div>
<div>Joey<br>
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<div><span>"colocated_variants": [<br>
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<div> {<br>
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<div> "allele_string": "A/G/T",<br>
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<div> "end": "69511",<br>
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<div> "frequencies": {<br>
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<div> "G": {<br>
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<div> "aa": "0.5441",<br>
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<div> "ea": "0.8874",<br>
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<div> "gnomad": "0.9506",<br>
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<div> "gnomad_afr": "0.6074",<br>
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<div> "gnomad_amr": "0.9508",<br>
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<div> "gnomad_asj": "0.9779",<br>
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<div> "gnomad_eas": "0.9995",<br>
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<div> "gnomad_fin": "0.9915",<br>
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<div> "gnomad_nfe": "0.9728",<br>
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<div> "gnomad_oth": "0.9499",<br>
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<div> "gnomad_sas": "0.9854"<br>
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<div> }<br>
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<div> },<br>
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<div> "id": "rs2691305",<br>
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<div> "start": "69511",<br>
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<div> "strand": "1"<br>
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<div> }<br>
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<div>]</div>
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<div><span>"colocated_variants": [<br>
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<div> {<br>
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<div> "AA": "T:0",<br>
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<div> "EA": "T:0.0006983",<br>
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<div> "allele_string": "C/A/G/T",<br>
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<div> "end": "105415607",<br>
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<div> "frequencies": {<br>
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<div> "G": {<br>
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<div> "afr": "0.0015",<br>
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<div> "amr": "0",<br>
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<div> "eas": "0.001",<br>
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<div> "eur": "0",<br>
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<div> "gnomad": "0.0002357",<br>
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<div> "gnomad_afr": "0.0002741",<br>
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<div> "gnomad_amr": "0.0005474",<br>
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<div> "gnomad_asj": "0",<br>
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<div> "gnomad_eas": "0.0004838",<br>
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<div> "gnomad_fin": "0",<br>
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<div> "gnomad_nfe": "1.384e-05",<br>
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<div> "gnomad_oth": "0",<br>
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<div> "gnomad_sas": "0.0006331",<br>
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<div> "sas": "0.0133"<br>
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<div> }<br>
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<div> },<br>
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<div> "id": "rs112699389",<br>
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<div> "minor_allele": "T",<br>
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<div> "minor_allele_freq": "0.0072",<br>
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<div> "start": "105415607",<br>
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<div> "strand": "1"<br>
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<div> }<br>
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<div>]<br>
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