[ensembl-dev] Quick question about --af_esp option in VEP
Laurent Gil
lgil at ebi.ac.uk
Mon Mar 4 09:12:00 GMT 2019
Hi Joey,
I was trying to guess the flags/options you used to replicate your results.
Out of curiosity, could you send us the command line you used, please ?
Best regards,
Laurent
Ensembl Variation
On 01/03/2019 17:03, Joseph A Prinz wrote:
> Hi Laurent,
>
> Thank you so much for your clarifications--this really helps.
>
> Also, I am quite sure that I am not using --no_check_alleles and according to the docs this should be off by default.
>
> Best,
> Joey
>
> ________________________________________
> From: Laurent Gil <lgil at ebi.ac.uk>
> Sent: Friday, March 1, 2019 6:28 AM
> To: Ensembl developers list; Joseph A Prinz
> Subject: Re: [ensembl-dev] Quick question about --af_esp option in VEP
>
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__www.ensembl.org_info_docs_tools_vep_script_vep-5Foptions.html-23opt-5Fno-5Fcheck-5Falleles&d=DwMD-g&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=MyiOXAbvDPHjfcbbrGErkARYNzXyIRtvJJwraJIIOZY&m=coWL8H6tj72DIVE5suen8RNbUPbnezlutD-vqx96vGA&s=6hdGNi3AaDVgeLlppEOAG-xZfn3baOP9TcdWsUotfIs&e=>". 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<mailto: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<mailto:Dev at ensembl.org>
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ensembl.org_mailman_listinfo_dev&d=DwMD-g&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=MyiOXAbvDPHjfcbbrGErkARYNzXyIRtvJJwraJIIOZY&m=coWL8H6tj72DIVE5suen8RNbUPbnezlutD-vqx96vGA&s=gs-SQoOqJD3RLWOgdQbk4r82iBHfib5ZgRkYRtMegyI&e=>
> Ensembl Blog: http://www.ensembl.info/<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ensembl.info_&d=DwMD-g&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=MyiOXAbvDPHjfcbbrGErkARYNzXyIRtvJJwraJIIOZY&m=coWL8H6tj72DIVE5suen8RNbUPbnezlutD-vqx96vGA&s=V4RXiOhQ2Ug5nw032a8TY3C7HmabUF9n0CaZe7qXmjI&e=>
>
More information about the Dev
mailing list