[ensembl-dev] VEP variants missing on output

[Will McLaren]

Hi Guillermo,

None of those options should filter out variants.

Are you able to provide any of the files that recreate the problem?

Is there any chance that you are using VCF input and it contains
non-variant lines - this would be where the ALT column is empty or "."? If
so, this may be your problem. To force these to be included in the output,
you should add --allow_non_variant.

Regards

Will


On 21 May 2013 09:40, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

>  Hello,
>
> I've been checking VEP results, and i've noticed that I'm missing some
> input variants in the output.
>
> I think this may be issued to some of the options i'm using to launch vep:
>
> hgvs               1
> canonical          1
> ccds               1
> check_svs          1
> domains            1
> gmaf               1
> hgnc               1
> maf_1kg            1
> numbers            1
> polyphen           b
> regulatory         1
> sift               b
>
> Should be any of these options filtering output? I've disabled all plugins
> to run this test to be sure that it's not a plugin issue.
>
>
>    - With a 406 variant input vcf file, I've missed 16 variants.
>     - I then ran VEP with only those 16 missing variants and missed 3 on
>    output.
>     - Rerun again and now with 3 missing variants and now not a single
>    one was missing.
>
> I would like to know what's behind that weird behaviour.
>
> Thank you.
>
> Best regards,
> Guillermo.
>
>
>
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