[ensembl-dev] UPLOADED_ALLELE is always output minimized for indels

[Likhitha Surapaneni]

Hi Ivan,

Sorry to hear that the functionality is not as expected. I am able to 
replicate the issue with the input and we will try to provide a fix in 
the coming release.

Kind regards,

Likhitha

On 07/08/2024 21:52, Adzhubey, Ivan A. wrote:
>
> Hi,
>
> VEP command line v112, run on Linux:
>
> Looks like, despite what the documentation says, UPLOADED_ALLELE field 
> is always output minimized in case of indels, rendering it useless. 
> See the full test input and VEP output files attached.
>
> # input file
> $ cat test.vcf
> ##fileformat=VCFv4.2
> ##source=test
> ##reference=GRCh38
> #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
> 1       961320  1:961320:G/GCAGGCTCGGCC G       GCAGGCTCGGCC    . 
>       PASS    .
>
> # the UPLOADED_ALLELE field contents in output is definitely NOT the 
> uploaded allele
> $ grep -v '^##' test.vep.tsv | cut -f15
> UPLOADED_ALLELE
> -/CAGGCTCGGCC
>
> Best,
>
> Ivan
>
> -- 
> Ivan Adzhubey, Ph.D.
> Research Associate
> Department of Biomedical Informatics
> Harvard Medical School
> 10 Shattuck Street, Suite 514
> Boston, MA 02115
> tel: (617) 432-2144
> fax: (617) 432-0693
> web:https://sunyaevlab.hms.harvard.edu/wiki/!web/start
>
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