Ensembl VEP analyses your variant alleles in detail using a flexible choice of options, but it can also create simple summary tables and graphics describing your full variant set.
On the VEP results web page, we display three sets of summary information. The table of counts tells you how many variants were annotated and if any were skipped (usually this is because they are malformed or mapped to a sequence which is not recognised). If you have compared your data to known variants and found some matches, the number and percentage of your variants that have been previously identified will be reported, alongside the number of genes, transcripts and regulatory features that your variants overlap. Pie charts show the proportions of total and coding consequences predicted: these are for each variant and feature combination, not for each individual variant.
You can also produce these plots with command line VEP and some extra plots too. The additional plots are: a pie chart showing the most severe consequence by variant, variant distribution by/along chromosomes and distribution within protein sequences. Raw counts are also available for each of these.
You can specify the name of the file to save the plots in, using the –stats_file [filename] option, where [filename] is an HTML file ending in .htm or .html. If you prefer the information in plain text, only use the –stats_text option. If you don’t need this information at all, use the –no_stats to see a slight speed up of your VEP analysis.