[ensembl-dev] loading VEP output into db

[Cyriac Kandoth]

Hi Will. Out of curiosity - do you know what is the most popular output
format among VEP users? And which one do you prefer we all use?

~C

On Wed, Jul 27, 2016 at 7:41 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hi Nikolas,
>
> As I mentioned in reply to your previous question, you can use --tab with
> VEP 84 or later, or in earlier versions use --fields to have all output
> written to separate tab-separated columns.
>
> The limitation of using --fields is that you must specify them manually,
> but you could do this once and save it to a configuration file [1] or as an
> ENV variable. You then have the benefit of knowing which columns you would
> need to create in your DB.
>
> Another option would be to use VCF output and a simple shell script to
> create one line per transcript.
>
> Regards
>
> Will
>
> [1] :
> http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_config
>
>
>
> On 27 July 2016 at 12:24, Nikolas Pontikos <n.pontikos at ucl.ac.uk<mailto:
> n.pontikos at ucl.ac.uk>> wrote:
> I'm looking for an easy way (with minimal reformatting) of loading the
> output of VEP into a database.
>
> So far I have tried loading the JSON output straight into mongo but
> was wondering if there was a simpler tab separated format with one
> transcript per line.
>
> Maybe I should resort to only retrieving the most severe transcript
> consequence per variant.
>
> I'd be happy to hear your suggestion.
>
> Many Thanks,
>
> Nikolas.
>
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