[ensembl-dev] VEP variants missing on output

[Guillermo Marco Puche]

Hello Will,

Here's the input: 
https://github.com/guillermomarco/vep_plugins_71/blob/master/missing_variants/missing_output_variants.vcf

As you said it's not about the options or plugins. Launching VEP without 
specyfiying any option still returns an output with missing variants.

Regards,
Guillermo.


On 05/21/2013 01:49 PM, Will McLaren wrote:
> 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 
> <mailto: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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