[ensembl-dev] Output gzip in VEP

[Will McLaren]

Hi Konrad,

There is such a flag, but it was put in exclusively for use by the webcode
and hence not documented as I figured most people would do as you suggest.

Adding --tabix when using --vcf bgzips and tabix indexes your output. Make
sure to name your output file *.gz using -o. Note, however, that an
uncompressed file is created first and then bgzipped - for some reason
tabix complains about bgzipped files created via piped output.

Regards

Will


On 20 May 2014 02:04, Konrad Karczewski <konradk at broadinstitute.org> wrote:

> Hi everyone,
>
> Is there a plan to generate a gzipped VCF in VEP any time soon? I know it
> can read it (which is fantastic, by the way) and I can always "vep ... |
> gzip" but it'd be really useful if there were a --output_gzip flag or
> something similar to output directly.
>
> -Konrad
>
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