[ensembl-dev] VEP command line

[Irina Armean]

Hi Margaret,


Sorry for the delay.

The stats written out in stats_html are collected internally 
simultaneously with the VEP annotation and therefore are not generated 
based on the VCF columns of the output file.


Depending on what VEP run options were selected, the counts could be 
reproduced based on the output file. For example the number of 
overlapped genes corresponds to the unique count of ENSG identifiers in 
the 'Gene' output column. The number of overlapped transcripts and 
regulatory features could be computed based on the 'Feature' and 
'Feature_type' columns.



Kind regards,

Irina


On 12/09/2019 19:27, Linan, Margaret wrote:
>
> Hi -
>
>
> Does anyone know how the VEP command line program's stats_html utility 
> calculates the following (i.e., what VCF columns and operations it uses)?
>
>     - VCF file pre-processing
>
>     - Number of overlapped genes
>
>     - Number of overlapped transcripts
>
>     - Number of overlapped regulatory features
>
>
> Thank you,
>
> Margaret
>
>
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