[ensembl-dev] VEP deleting everything after CSQ

[Will McLaren]

Bug is fixed on release/76 branch of ensembl-variation now anyway.

Will


On 26 August 2014 14:33, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hi Konrad,
>
> Thanks for spotting that, definitely a bug.
>
> You can have the VEP keep the original CSQ field using --keep_csq which
> sort of bypasses the problem, though I'm not sure if the resulting VCF with
> two CSQ entries violates VCF spec.
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
>
> On 26 August 2014 14:22, Konrad Karczewski <konradk at broadinstitute.org>
> wrote:
>
>>  Hi dev team,
>>
>> I've run into what appears to be a bug in VEP. If you already have a CSQ
>> field in a VCF, VEP is supposed to overwrite it (which it does properly).
>> However, I ran into the case where I had an old CSQ field (that I wanted to
>> update) followed by additional fields, and VEP appears to delete these
>> additional fields! (Additionally, it seems to introduce an additional
>> semicolon sometimes, but that's obviously not as big a deal). Example VCF:
>>
>>  1       739142  rs2340527       T       A       1        PASS
>> AC=5;CSQ=||||;AN=100
>>
>>  results in:
>>
>>  1       739142  rs2340527       T       A       1       PASS
>> AC=5;;CSQ=A|ENSG00000237491|ENST00000588951|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||1/3||||||1|||RP11-206L10.9|Clone_based_vega_gene|||-:0.0303|lincRNA||||||||||||,A|ENSG00000237491|ENST00000429505|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||1/2||||||1|||RP11-206L10.9|Clone_based_vega_gene|||-:0.0303|lincRNA||||||||||||,A|ENSG00000237491|ENST00000591440|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||1/2||||||1|||RP11-206L10.9|Clone_based_vega_gene|||-:0.0303|lincRNA||||||||||||,A|ENSG00000237491|ENST00000590848|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||3/4||||||1|||RP11-206L10.9|Clone_based_vega_gene|||-:0.0303|lincRNA||||||||||||,A|ENSG00000237491|ENST00000589531|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||1/3||||||1|||RP11-206L10.9|Clone_based_vega_gene|||-:0.0303|lincRNA||||||||||||,A|ENSG00000230092|ENST00000590817|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||3/3||||||-1|||RP11-206L10.8|Clone_based_vega_gene|||-:0.0303|transcribed_unprocessed_pseudogene||||||||||||,A|ENSG00000237491|ENST00000586288|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||4/6||||||1|||RP11-206L10.9|Clone_based_vega_gene|||-:0.0303|lincRNA||||||||||||,A|ENSG00000237491|ENST00000587530|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||2/3||||||1|||RP11-206L10.9|Clone_based_vega_gene|||-:0.0303|lincRNA||||||||||||,A|ENSG00000230092|ENST00000447500|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||3/3||||||-1||YES|RP11-206L10.8|Clone_based_vega_gene|||-:0.0303|processed_transcript||||||||||||,A|ENSG00000237491|ENST00000593022|Transcript|intron_variant&nc_transcript_variant||||||rs200911849|||1||1/3||||||1|||RP11-206L10.9|Clone_based_vega_gene|||-:0.0303|lincRNA||||||||||||
>>
>>  and AN=100 is nowhere to be found.
>>
>> -Konrad
>> -Konrad
>>
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>
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