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Problem with "Unknown option: af_gnomad"

Open MjelleLab opened this issue 2 years ago • 1 comments

I have a problem with VEP it seems. Complaining about Unknown option: af_gnomad

perl ~/software/vcf2maf-1.6.21/vcf2maf.pl --ref-fasta /home/local/xxxx/.vep/homo_sapiens/102_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz --input-vcf PANCNGS-006.vcf --output-maf PANCNGS-006.vcf.maf --tumor-id T-PANCNGS-006 --normal-id N-PANCNGS-006 --vep-path /home/local/xxxx/anaconda3/bin STATUS: Running VEP and writing to: ./PANCNGS-006.vep.vcf Unknown option: af_gnomad ERROR: Failed to parse command-line flags

ERROR: Failed to run the VEP annotator! Command: /home/local/xxxx/anaconda3/bin/perl /home/local/xxxx/anaconda3/bin/vep --species homo_sapiens --assembly GRCh37 --no_progress --no_stats --buffer_size 5000 --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --canonical --protein --biotype --uniprot --tsl --variant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --vcf --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --dir /home/local/robinm/.vep --fasta /home/local/xxxx/.vep/homo_sapiens/102_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz --format vcf --input_file PANCNGS-006.vcf --output_file ./PANCNGS-006.vep.vcf --offline --pubmed --fork 4 --polyphen b --af --af_1kg --af_esp --af_gnomad --regulatory

MjelleLab avatar Oct 29 '21 09:10 MjelleLab

I was getting the same error Unknown option: af_gnomad. But when tried with VEP version 103.1, it worked.

asntech avatar Jul 18 '22 12:07 asntech