Entering edit mode
6.7 years ago
bruce.moran
▴
960
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
Thanks Emily. Out of curiosity, was that the default previously? I had just updated old scripts which never had that flag.
I don't think it was, but I could be wrong.