[ensembl-dev] Quick question about --af_esp option in VEP

[Joseph A Prinz]

Hi VEP devs,

I wanted to confirm the output of --af_esp when using JSON output.

Some times I see values represented 'aa' and 'ea' nested under 'frequencies', and sometimes I see values "AA" and "EA" not nested under 'frequencies'.
Further when appearing as "AA" / "EA" the values do not seem to be parsed in the same way (they appear as "allele:frequency").

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.

Below are examples of both scenarios.

Thanks for taking a look!
Joey

"colocated_variants": [
  {
    "allele_string": "A/G/T",
    "end": "69511",
    "frequencies": {
      "G": {
        "aa": "0.5441",
        "ea": "0.8874",
        "gnomad": "0.9506",
        "gnomad_afr": "0.6074",
        "gnomad_amr": "0.9508",
        "gnomad_asj": "0.9779",
        "gnomad_eas": "0.9995",
        "gnomad_fin": "0.9915",
        "gnomad_nfe": "0.9728",
        "gnomad_oth": "0.9499",
        "gnomad_sas": "0.9854"
      }
    },
    "id": "rs2691305",
    "start": "69511",
    "strand": "1"
  }
]

"colocated_variants": [
  {
    "AA": "T:0",
    "EA": "T:0.0006983",
    "allele_string": "C/A/G/T",
    "end": "105415607",
    "frequencies": {
      "G": {
        "afr": "0.0015",
        "amr": "0",
        "eas": "0.001",
        "eur": "0",
        "gnomad": "0.0002357",
        "gnomad_afr": "0.0002741",
        "gnomad_amr": "0.0005474",
        "gnomad_asj": "0",
        "gnomad_eas": "0.0004838",
        "gnomad_fin": "0",
        "gnomad_nfe": "1.384e-05",
        "gnomad_oth": "0",
        "gnomad_sas": "0.0006331",
        "sas": "0.0133"
      }
    },
    "id": "rs112699389",
    "minor_allele": "T",
    "minor_allele_freq": "0.0072",
    "start": "105415607",
    "strand": "1"
  }
]





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