[ensembl-dev] VEP 92 not so verbose ?

[Andrew Parton]

Hi,

I’ve had a look at v92.1 and v87 of VEP and I’m unable to replicate your issue - could you please send me the output you currently get with the —verbose flag for both versions?

Kind Regards,
Andrew

> On 12 May 2018, at 12:48, João Eiras <joao.eiras at gmail.com> wrote:
> 
> Hi.
> 
> I've upgraded VEP in my pipeline, and I'm somehow having trouble
> getting it to be chatty about what it is doing. I'm calling it like
> this:
> 
> $ perl $vep_dist/vep \
>  -i a.vcf --format vcf \
>  --cache --offline --merged \
>  --species mus_musculus --assembly GRCm38 \
>  --force_overwrite --verbose \
>  --dir $vep_cache \
>  -o a.vcf.txt \
> 
> Input a.vcf:
> ##fileformat=VCFv4.1
> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
> chr1 99772782 . A T 5000 . . .
> 
> Output a.vcf.txt:
> ## ENSEMBL VARIANT EFFECT PREDICTOR v92.1
> ## ...
> 
> So, the command runs correctly, but even though the --verbose flag is
> passed I see nothing in the output. There is one mention of the
> verbose flag in the docs at
> http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html and
> this flag worked just fine in version 87.
> 
> The previous versions of VEP would report input configuration and
> progress information regarding handling of the input data.
> 
> So, has the flag been removed ?
> 
> Thank you !
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