[ensembl-dev] VEP deleting everything after CSQ

[Will McLaren]

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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