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🔍 plugin-inspect

plugin-inspect is a diagnostic tool included in the vep-polaris toolkit. It scans VEP plugin data files to check for:

  • Whether files contain usable data (non-comment lines)
  • What chromosome format they use (e.g., chr1 vs 1)
  • Whether any files may cause problems with VEP annotation due to format mismatches

🧠 Why This Tool Exists

Ensembl VEP is strict about chromosome naming. If your input VCF uses chr1 but a plugin file uses 1, annotations may silently fail or be skipped. plugin-inspect helps detect and prevent these issues.

🛠️ Usage

vep-polaris plugin-inspect [--dir /path/to/plugins] [--no-color] [--help]

Options

Option Description
--dir Directory containing plugin data files (default: ~/vep/Plugins)
--no-color Disables ANSI color codes (useful for logging)
--help Shows usage information

📄 Example Output

🔍 Scanning plugin data files in: /vep/Plugins
-------------------------------------------------------------
File                                      | Chromosome Format    | Header/First Line
-------------------------------------------------------------
revel_ready.tsv                           | N                    | 1  35142  35142  GA ...
spliceai_scores.masked.snv.hg37.vcf.gz   | chrN                 | >chr1
whole_genome_SNVs.tsv.gz                 | ❓ Unknown            | ⚠️ Empty or comment-only file...

📦 File Types Supported

plugin-inspect scans files with the following extensions:

  • .tsv, .txt, .dat, .gz

🧰 Use Cases

  • Before running VEP on a new dataset
  • When adding or updating plugin files
  • During plugin development or debugging
  • As part of a CI pipeline to validate plugin integrity

🧪 Tests

See the testing documentation to learn how to run automated test coverage for this tool.