[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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