How to export or visualize the data after adding annotations using vep()


#1

Hello everyone,

I am trying to export the data to a vcf file or a csv file after adding annotations using vep()

I used the following line to add annotations to my vcf file and it looked like it worked because when i used describe( ), i was able to see the structure.

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

But when i tried vcf_file.vep.show ( ) i got the following error. I also tried to export the data to vcf or text, i got the same following error.

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

It would be great, if someone could help me with this.
Thanks in advance.