[ensembl-dev] Variation (VEP) 2.5 - Het/Hom Output - Plugin Attached

[Will McLaren]

Hi Ricardo,

I had to add a little bit of code to the ensembl-variation API CVS
tree to get this to work - you'll need to update your
ensembl-variation module checkout using "cvs update" in that
directory. This bit of code gives you the $vf->{genotype} when you ask
for it in the plugin.

The allele_string method, as Sarah points out, won't work as you
expect, as this string just stores the given possible alleles for this
variant; it does not store the observed genotype for an individual.
Both a non-reference hom genotype and a het genotype will look the
same in the allele_string field.

Cheers

Will

On 22 May 2012 12:19, Ricardo Parolin Schnekenberg
<ricardos at well.ox.ac.uk> wrote:
>
> Hi Sarah,
>
> Thanks for the input.
>
> I don't know if I have the very latest version. I downloaded it from the
> official website
> http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-tools/scripts/variant_effect_predictor.tar.gz
> on the day release-67 was uploaded to the FTP server. (May 8th I guess?).
>
> No, Will's version using transcript_variation->variation_feature->genotype
> didn't work for me. But maybe it is just my ignorance in object-oriented
> programming.
>
> However, using the allele_string it DOES work, at least for my version,
> because I do see HOM and HET lines in the output and I both manually
> checked >20+ lines of each in the original vcf file and compared to the
> output of VEP. I would post the output of all this but all our servers are
> down at the moment =/
>
>
>
> --
> Ricardo Parolin Schnekenberg
> Genomics Research
> Wellcome Trust Centre for Human Genetics
> University of Oxford
>
>
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