Missing annotations for BND variants.

[ramprasadn]

Describe the issue

Some BND variants are missing vep annotations, while the rest have them.

Additional information

System

• VEP version: 113
• VEP Cache version: 113

Full VEP command line

vep \
    -i justhusky_view.vcf \
    -o justhusky_svdbquery_vep.vcf.gz \
    --dir_plugins cache/Plugins --plugin pLI,pLI_values.txt --appris \ 
    --biotype --buffer_size 100 --canonical --cache --ccds --compress_output bgzip \
    --distance 5000 --domains --exclude_predicted --force_overwrite --format vcf --fork 4 \
    --hgvs --humdiv --max_sv_size 248956422 --merged --no_progress --numbers --per_gene\
    --polyphen p --protein --off \
    --fasta reference.fasta \
    --assembly GRCh37 \
    --species homo_sapiens \
    --cache \
    --cache_version 113 \
    --dir_cache ${PWD}/cache \
    --fork 4

Full error message

2024-10-22 10:19:00 - INFO: BAM-edited cache detected, enabling --use_transcript_ref; use --use_given_ref to override this

Data files (if applicable)

They include:

• The input file: (This file is bgzip compressed as github doesn't support vcf file upload, but to clarify, I ran the uncompressed version of this file with vep)
  justhusky_view.vcf.gz

• The output file: justhusky_svdbquery_vep.vcf.gz

[likhitha-surapaneni]

Hi @ramprasadn, thank you for providing us the files. We are currently investigating this, the affected annotations seem to be for breakpoints overlapping intergenic variants.