vip-annotate

Variant Call Format (VCF) file annotation

Requirements

• Operating system: Linux
• CPU: x86-64-v3 compatible
• Container runtime: Apptainer ≥ 1.4.5

Usage

vip-annotate --help

Usage:
  vip-annotate [OPTIONS] <command> [ARGS...]
  vip-annotate --version
  vip-annotate --help

Options:
  -d, --debug       Enable debug logging

Commands:
  annotate          Annotate vcf using an annotation database
  database-build    Build annotation database
  database-download Download annotation download

Report bugs and questions at https://github.com/molgenis/vip-annotate/issues

Command: annotate

vip-annotate annotate --help

Usage:
  vip-annotate annotate --annotations DIR --input FILE --output FILE [OPTIONS]
  vip-annotate annotate --help

Options:
  -a, --annotations DIR       Directory containing annotation database  (required)
  -i, --input       FILE      Input VCF file path; use '-' for stdin    (required)
  -o, --output      FILE      Output VCF file path; use '-' for stdout  (required)

  -O, --output-type v|z[0-9]  Output format                             (default: z)
                                Options:
                                  v      Uncompressed VCF
                                  z      Compressed VCF (default compression)
                                  z0-z9  Compressed VCF with compression levels 0-9

  -f, --force                 Overwrite existing output file if it exists

Command: database-download

vip-annotate database-download --help

Usage:
  vip-annotate database-download --output DIR [OPTIONS]
  vip-annotate database-download --help

Options:
  -o, --output      DIR      Output directory  (required)
  -f, --force                Overwrite existing output files if they exist

Command: database-build

vip-annotate database-build --help

Usage:
  vip-annotate database-build --definition <FILE> --input <FILE> [OPTIONS]
  vip-annotate database-build --help

Options:
  -d, --definition    FILE  Defines how to build the annotation database from input  (required)
  -i, --input         FILE  Input file path                                          (required)
  -o, --output        FILE  Output .vdb file path
  -f, --force         Overwrite existing output file if it exists

Definition

TODO

Development

Requirements

• Container runtime: Apptainer ≥ 1.4.5
• GraalVM 25
• Maven 3.9.16
• Set Maven property env=dev to activate dev and dev-<os> profiles.