[ensembl-dev] Diffrence in results of online and standalone API version of variant effect predictor

Will McLaren wm2 at ebi.ac.uk
Mon Feb 28 11:40:28 GMT 2011

Hi Ketan,

The online version of the VEP has a 750 variant limit - it sounds like
this might be the cause of the missing results.

The online version will provide you with results for the first 750
variants in your file, but not for those after this.

You should also note that if a variant does not fall within range
(5kb) of any transcripts, it is considered to be "intergenic" and will
not return any results at all.



On 26 February 2011 09:50, ketan padiya <ketanmicro at gmail.com> wrote:
> Hi!
> I used online variant effect predictor for variant analysis and downloaded
> results, then i also used variant effect predictor perl script API from my
> pc providing vcf file and i got the result.
> But when i compare both results i find many variants (skipped in one file
> and present in other file) are not common in files, i think they should be
> there.
> My vcf file did contain 1758 variants (rows) but using perl script API
> version applying -w mode only gave annotation for 1053 variants.
> Why this differences are there?
> Thanks.
> --
> Ketan Padiya
> Research Fellow
> Anand Veterinary College
> Gujarat
> India.
> +91 9428969448
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