--maf_exac flag not found in VEP77
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5.4 years ago
arronslacey ▴ 280

Hi,

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?

Thanks

VEP variant effect predictor exac • 1.2k views
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5.4 years ago

The --maf_exac command was only introduced into the VEP in release 83. Please update to the latest version to use this command.

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thank you emily this worked. It's been a while since I used VEP, but re-cloning the github I didn't realise there were plugins - good day for me!

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