Question: --maf_exac flag not found in VEP77
0
gravatar for arronslacey
3.9 years ago by
arronslacey260
United Kingdom
arronslacey260 wrote:

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

ADD COMMENTlink modified 3.9 years ago by Emily_Ensembl20k • written 3.9 years ago by arronslacey260
3
gravatar for Emily_Ensembl
3.9 years ago by
Emily_Ensembl20k
EMBL-EBI
Emily_Ensembl20k wrote:

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

ADD COMMENTlink written 3.9 years ago by Emily_Ensembl20k

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!

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by arronslacey260
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2367 users visited in the last hour