CLI Module

The command-line interface module provides the main entry point for VariantCentrifuge.

Command-line interface for VariantCentrifuge.

variantcentrifuge.cli.main()[source]

Run main entry point for variantcentrifuge CLI.

Return type:

None

Steps:

  1. Parse arguments.

  2. Configure logging and load config.

  3. Validate mandatory parameters (reference, filters, fields).

  4. Validate input files (VCF, phenotype).

  5. Update configuration with CLI parameters.

  6. Run the pipeline.

Changes for presets:

  • Added a –preset argument which allows specifying one or more predefined filters.

  • If multiple presets are chosen, they are combined with AND (&).

  • If user-specified filters are also provided, they are combined with these presets using AND.

  • Presets must be defined in config.json under “presets”.

Changes for sample substring removal:

  • Added a –remove-sample-substring argument which, if provided, removes the specified substring from all sample names extracted from the VCF before any comparisons or mappings.

Changes for links:

  • Added a –no-links argument to disable adding link columns. By default, links are added.

Changes for custom columns:

  • Added a –add-column argument which can be given multiple times to append columns with given headers (but blank values) to the final output.

Changes for transcript filtering:

  • Added a –transcript-list and –transcript-file argument which allows specifying one or more transcript IDs (by comma-separated list or a file with one transcript ID per line).

  • If provided, these transcripts are used to construct a SnpSift filter expression that filters variants by EFF[*].TRID field.

New changes for extra sample fields in genotype:

  • Replaced the old two-flag logic with a single –append-extra-sample-fields flag that optionally takes zero or more fields. If this flag is used with no arguments, it simply enables genotype+field appending with no extra fields. If arguments (space-separated) are provided, those fields are appended (e.g. DP, AD).

  • We retain –extra-sample-field-delimiter to control the delimiter between genotype and extra fields (default ‘:’).