[ensembl-dev] ALLELE_NUM issue

Will McLaren wm2 at ebi.ac.uk
Mon Aug 24 14:00:16 BST 2015


Hi Konrad,

The --minimal flag is resolving both ALTs to "C", so the code I had in
place which was a hash indexed on the resolved allele won't work in this
case.

I've had to refactor the code for how the allele number is determined, so
I'm reluctant to push this fix to a release branch.

It is on master, however, and should you wish to grab the fix for your
checkout, you could cherry-pick the commit to your ensembl-variation git
checkout:

cd ~/src/ensembl-variation
git fetch
git cherry-pick 0013c9e

Or if you don't want to go the cherry pick way, you'll need to replace the
following files with those from master:

modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
modules/Bio/EnsEMBL/Variation/VariationFeatureOverlap.pm
modules/Bio/EnsEMBL/Variation/VariationFeatureOverlapAllele.pm

Thanks again for the bug reports

Will

On 22 August 2015 at 17:22, Konrad Karczewski <konradk at broadinstitute.org>
wrote:

> Hi Will, Ensembl/VEP folk,
>
> I'm getting a weird multi-allelic issue in VEP v81 - when I annotate the
> below VCF, all annotations for the first site get an ALLELE_NUM of 2, which
> results in G->C being annotated as a frameshift (works fine when the SNV is
> on its own). Any ideas why this might be happening?
>
> -Konrad
>
> ##fileformat=VCFv4.1
> #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
> 1 898175 . G GC,C . . . .
> 1 898175 . G C . . . .
>
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