Open ramprasadn opened 4 days ago
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.
Hi @likhitha-surapaneni! Thank you for the update. I'm glad to hear you're looking into it. If you need any further information, just let me know.
Describe the issue
Some BND variants are missing vep annotations, while the rest have them.
Additional information
System
Full VEP command line
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