[ensembl-dev] VEP: --minimal doesn't seem to do its thing

[Cyriac Kandoth]

This might be limited to VCFs. I haven't tested it on other input formats.
Here 2 sample variants that I ran through VEP in offline cached mode...

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
 TUMOR   NORMAL
1       198498326       .       ATATAT  ATATATAT        .       .       .
    GT:AD:DP        0/1:10,10:20       0/0:30,5:35
1       198498325       .       AATATAT A,AATATATAT     .       .       .
    GT:AD:DP        0/2:10,0,10:20  0/0:30,0,5:35

Here is the full command used:
perl variant_effect_predictor.pl --species homo_sapiens --assembly GRCh37
--offline --no_progress --no_stats --sift b --ccds --uniprot --hgvs
--symbol --numbers --domains --regulatory --canonical --protein --biotype
--uniprot --tsl --pubmed --variant_class --shift_hgvs 1 --check_existing
--check_alleles --check_ref --total_length --allele_number --no_escape
--xref_refseq --failed 1 --vcf --minimal --flag_pick_allele --pick_order
canonical,tsl,biotype,rank,ccds,length --dir <vep_data> --fasta <ref_fasta>
--input_file <input_vcf> --output_file <output_vcf>

This is the way I would expect the output VCF to be re-formatted...

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
 TUMOR   NORMAL
1       198498331       .       T  TAT        .       .       .
GT:AD:DP        0/1:10,10:20       0/0:30,5:35
1       198498325       .       AATATAT A,AATATATAT     .       .       .
    GT:AD:DP        0/2:10,0,10:20  0/0:30,0,5:35

Thanks,
Cyriac
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