What is the setup required to perform annotations using vep?


#1

Hello everyone,

I am trying to add annotations to my vcf file using vep.

I used the following line to configure vep while creating my cluster on google cloud ( I am using windows 10)

–initialization-actions “gs://dataproc-initialization-actions/jupyter/jupyter.sh,gs://dataproc-initialization-actions/conda/bootstrap-conda.sh,gs://hail-common/cloudtools/init_notebook1.py,gs://hail-common/vep/vep/vep85-init.sh” ^

And i used the following line to add annotations to my vcf file

result = hl.vep(vcf_file, “gs://hail-common/vep/vep/vep85-gcloud.json”)

Then i received following error while trying to export the data. I am wondering if i need any additional setup for vep.
Thanks in advance.

Hail version: devel-0643c11962e8
Error summary: HailException: vep command ‘/usr/bin/perl /vep/variant_effect_predictor/variant_effect_predictor.pl --format vcf --json --everything --allele_number --no_stats --cache --offline --dir /vep --fasta /vep/homo_sapiens/85_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --minimal --assembly GRCh37 --plugin LoF,human_ancestor_fa:/vep/loftee_data/human_ancestor.fa.gz,filter_position:0.05,min_intron_size:15,conservation_file:/vep/loftee_data/phylocsf.sql -o STDOUT’ failed with non-zero exit status 2