cache 1
dir_cache  /data
assembly 'GRCh38'
offline 1
force_overwrite 1
custom file=/opt/vep/.vep/Cosmic_GenomeScreensMutant_v103_GRCh38.vcf.gz,short_name=COSMIC,format=vcf,type=exact,fields=LEGACY_ID%CNT

# Functional impact predictions
sift b # CALCULATE 1 - score
polyphen b # THESE TWO CAN BE AVERAGED

plugin REVEL,/opt/vep/.vep/REVEL/new_tabbed_revel_grch38.tsv.gz
# TODO: CALCUALTE THEIR L2 NORM
# plugin CADD,/opt/vep/.vep/CADD/GRCh38/whole_genome_SNVs.tsv.gz,/opt/vep/.vep/CADD/GRCh38/InDels.tsv.gz


# Clinical significance
check_existing
clinvar

# Allele frequencies
af
af_1kg
af_gnomade
af_gnomadg
max_af

# Additional useful flags
numbers
hgvs
symbol
canonical