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

[Adzhubey, Ivan A.]

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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