[ensembl-dev] VEP: --vcf_info_field ANN only seems to change VCF header, not INFO

Cyriac Kandoth kandoth at cbio.mskcc.org
Fri Aug 14 02:13:13 BST 2015


This is the command used:
perl variant_effect_predictor.pl --species homo_sapiens --assembly GRCh37
--offline --quiet --no_stats --everything --shift_hgvs 1 --check_existing
--check_alleles --check_ref --total_length --allele_number --no_escape
--xref_refseq --failed 1 --vcf --vcf_info_field ANN --flag_pick_allele
--pick_order canonical,tsl,biotype,rank,ccds,length --dir $vep_data --fasta
$ref_fasta

Where $vep_data and $ref_fasta are paths to the offline cache and reference
fasta respectively.

~Cyriac
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