Ensembl VEP 89 Output Format

Question

[bruce.moran]

I have just updated to VEP v89 from v81. Previously the output was an annotated VCF, but now it is a strange, new format. Can someone advise on how to get the former?

Thanks,

Bruce.

command:

VCF="input.vcf"
OUT=$(echo $VCF | sed 's/vcf/VEP89.vcf/')
STATS=$(echo $VCF | sed 's/vcf/VEP89.stats/')

${HOME}/ensembl-vep/vep \
    --cache \
    --offline \
    --merged \
    --fork 12 \
    --gencode_basic \
    --everything \
    --total_length \
    --allele_number \
    --no_escape \
    --check_existing \
    --xref_refseq \
    --variant_class \
    --dir ${HOME}/.vep \
    --fasta ${HOME}/human_g1k_v37.fasta \
    --assembly GRCh37 \
    --force_overwrite \
    --input_file $VCF \
    --output_file $OUT \
    --stats_file $STATS \
    --stats_text

Answer 1

[Emily]

--vcf will give you output in VCF

[bruce.moran]

Thanks Emily. Out of curiosity, was that the default previously? I had just updated old scripts which never had that flag.

[Emily]

I don't think it was, but I could be wrong.