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

Joseph A Prinz joseph.prinz at duke.edu
Thu Feb 28 20:28:41 GMT 2019


A follow-up:

I am also seeing oddly parsed frequencies for 'gnomAD' see below.

I am using VEP version 95.1

Thanks again,
Joey

'colocated_variants': [
{ 'AA': '-:0.02651',
 'EA': '-:0.02891',
 'allele_string': 'A/-',
 'end': '36785668',
 'gnomAD': '-:0.1349',
 'gnomAD_AFR': '-:0.104',
 'gnomAD_AMR': '-:0.1808',
 'gnomAD_ASJ': '-:0.1746',
 'gnomAD_EAS': '-:0.1653',
 'gnomAD_FIN': '-:0.09683',
 'gnomAD_NFE': '-:0.1172',
 'gnomAD_OTH': '-:0.1465',
 'gnomAD_SAS': '-:0.1864',
 'id': 'rs756392461',
 'start': '36785668',
 'strand': '1'},
{ 'AA': 'AA:0.01702,-:0.02651',
 'EA': 'AA:0.01386,-:0.02891',
 'allele_string': 'A/AA/-',
 'end': '36785668',
 'gnomAD': '-:0.1349,AA:0.05111',
 'gnomAD_AFR': '-:0.104,AA:0.05793',
 'gnomAD_AMR': '-:0.1808,AA:0.08017',
 'gnomAD_ASJ': '-:0.1746,AA:0.05098',
 'gnomAD_EAS': '-:0.1653,AA:0.08157',
 'gnomAD_FIN': '-:0.09683,AA:0.029',
 'gnomAD_NFE': '-:0.1172,AA:0.03693',
 'gnomAD_OTH': '-:0.1465,AA:0.05941',
 'gnomAD_SAS': '-:0.1864,AA:0.08409',
 'id': 'TMP_ESP_2_36785668_36785668',
 'start': '36785668',
 'strand': '1'}
]




________________________________________
From: Joseph A Prinz
Sent: Thursday, February 28, 2019 12:42 PM
To: dev at ensembl.org
Subject: Quick question about --af_esp option in VEP

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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