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

[Laurent Gil]

Dear Joseph,

Thank you for reporting this.


By default/design the JSON output only displays in "frequency" the 
frequencies related to the alternative allele(s) you used in your input 
file, e.g. :


# Your input:

     14:105415607 C/*G*

# Your output:

     "AA": "T:0",
     "EA": "T:0.0006983",

     "frequencies": {

           "*G*": {
             "afr": "0.0015",
             "amr": "0",
             "eas": "0.001",
             "eur": "0",

             "gnomad": "0.0002357",

             ...}

     },

     "allele_string": "C/A/*G*/T",

     "id":"rs112699389"


However it also returns the corresponding minor allele frequency for ESP 
populations in a separate part of the JSON if the alternative differs 
from your alternative allele. In the example above, the alternative 
allele for rs112699389 in the ESP populations is T.



For the second issue, it looks like you are using the flag 
"--no_check_alleles 
<https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_no_check_alleles>". 
This flag doesn't compare which is/are your input alternative allele(s) 
with the co-located alleles and simply list the frequencies of each 
alternative allele of the co-located variants, e.g.:


# Input:

     2:36785668 A/T

# Output:

     "AA":"*AA*:0.01702,-:0.02651",
     "EA":"*AA*:0.01386,*-*:0.02891",
     "gnomAD_SAS":"*-*:0.1864,*AA*:0.08409",
     "gnomAD_OTH":"*-*:0.1465,*AA*:0.05941",
     "gnomAD_EAS":"*-*:0.1653,*AA*:0.08157",
     "gnomAD_ASJ":"*-*:0.1746,*AA*:0.05098",
     "gnomAD_AMR":"*-*:0.1808,*AA*:0.08017",
     "gnomAD":"*-*:0.1349,*AA*:0.05111",
     "gnomAD_NFE":"*-*:0.1172,*AA*:0.03693",
     "gnomAD_FIN":"*-*:0.09683,*AA*:0.029",
     "allele_string":"A/*AA*/*-*",

     "id":"TMP_ESP_2_36785668_36785668",



I agree that these different ways to display the frequencies of the 
co-located variants can be confusing and we will try to make it easier 
to read/parse.


Best regards,

Laurent
Ensembl Variation

On 28/02/2019 20:28, Joseph A Prinz wrote:
> 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"
>   }
> ]
>
>
>
>
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20190301/448d7a11/attachment.html>