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

[Ricardo Parolin Schnekenberg]

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