I would like to get the exac allele frequencies by using the --maf_exac flag in VEP.
My install of VEP included building a cache from homo_sapiens_vep_77_GRCh38.tar.gz
After letting the installer script build the cache, I then tried:
perl variant_effect_predictor.pl -i myinput.txt -o myoutput.vcf --cache --maf_exac --polyphen p --sift p
to which I got:
Unknown option: maf_exac ERROR: Failed to parse command-line flags
It seems that although I am using --maf_exac in conjunction with a cache as recommended in the documentation, VEP is not recognizing --maf_exac as a valid input.
Is there a problem with my command?