[ensembl-dev] vep.pl filter questions

[Will McLaren]

Hi Poorva,

I would recommend that you post-filter your results using filter_vep.pl
[1], something like:

perl filter_vep.pl -filter "ExAC_AF < 0.01 or not ExAC_AF" -i
variant_effect_output.txt

This offers more flexibility that the runtime filtering offered by the
--freq_* flags.

Regards

Will McLaren
Ensembl Variation

[1] : http://www.ensembl.org/info/docs/tools/vep/script/vep_filter.html

On 3 March 2017 at 16:43, Mudgal, Poorva <poorva at email.unc.edu> wrote:

> Hi,
>
>
>
> I work at UNC chapel hill as a Data manager and have used vep.pl lately.
> We are happy to see the frequencies in numbers rather allele:frequency. I
> have questions regarding the filters associated with the vep.pl
>
>
>
> 'freq_filter=s', # exclude or include
>
>
>
> 'freq_freq=f', # frequency to filter on
>
>
>
> 'freq_gt_lt=s', # gt or lt (greater than or less than)
>
> 'freq_pop=s', # population to filter on
>
>
>
> Can you please tell me if string or number to be used for above filters?
> Also we are mostly interested in applying filters on ExAC column (e.g.
> ExAC_AF_POPMAX < 0.01 or isMissing(ExAC_AF_POPMAX) ). Looking forward to
> hearing from you.
>
>
>
> Thanks,
>
> Poorva
>
>
>
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