Missing annotation of intergenic region, --distance doesn't help

[dshafranskaya]

Describe the issue

The variant (chr18:63096725, CAGCCGAAACCC[chr14:105897961[) did not receive annotation after running VEP. Although custom annotation covers this region, the string representing this variant lacks the CSQ field entirely. The distance from this coordinate to the start of BCL2 (chr18:63,123,346-63,320,128) is approximately 26,000 nucleotides.

Is it possible to make VEP apply custom annotations in all cases, even when a coordinate is in an intergenic region not covered by the reference? Or, how should I use the --distance parameter to annotate this coordinate?

Additional information

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System

• VEP version: 112
• VEP Cache version: 112
• Perl version:
• OS: Docker image ubuntu:20.04
• tabix installed ?

Full VEP command line

./vep --assembly GRCh38 --cache --custom file=[PATH]/ig_rearrangements.bed.gz,format=bed,short_name=CUSTOM_SYMBOL --database 0 --dir_cache /mnt --distance 30000 --force_overwrite --format vcf --input_file gridss-RS005716.vcf --no_stats --offline --output_file [PATH]/output.vcf --vcf

Full error message

Including the warnings, if available

Data files (if applicable)

They include:

• The input file
• The output file
• The custom file(s)
  You can provide a sample of them