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Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
Apache License 2.0
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--exclude_predicted #1686

Closed jammywwh closed 2 weeks ago

jammywwh commented 1 month ago

When I tested vep annotations, I found that with or without the --exclude_predicted option, the results came out without predicted transcripts. This problem exists with the hg19 genome, but not with the hg38 genome.

System

Full VEP command line

vep \
  -i case.vcf \
  --dir_cache /datapool/db/vep/cache/ --offline --cache \
  --species homo_sapiens \
  --assembly GRCh37 \
  --fasta ucsc.hg19.opn1masked.fasta \
  --refseq \
  --fork 4 \
  --plugin UTRannotator,/datapool/db/vep/uORF/uORF_5UTR_GRCh37_PUBLIC.txt \
  --tab --force_overwrite \
  -o utrAnno.txt
olaaustine commented 1 month ago

Hi @jammywwh, Hope this meets you well? If possible can you share your input VCF file or example of variants with this issue. Thank you very much Ola.

jammywwh commented 4 weeks ago

Hi, @olaaustine Thanks for your reply. input.vcf is input vcf file, output.txt is annotated output file. files.zip

Thank you. Jammy.

olaaustine commented 2 weeks ago

Hi @jammywwh, Hope this meets you well? I have been able to recreate this issue. Unfortunately, we do not support the use of --exclude_predicted for GRCh37. We will add this to the documentation to reflect this. Thank you Ola.

jammywwh commented 2 weeks ago

Hi, @olaaustine Thanks for your reply. I got it. Best wishes, Jammy