Extractor Module

VCF field extraction utilities

Field extraction module.

This module uses SnpSift extractFields to extract specific fields from VCF records and save the result to the specified output file.

variantcentrifuge.extractor.extract_fields(variant_file, fields, cfg, output_file)[source]

Extract specified fields from variant records.

Write them directly to output_file, controlling the SnpSift field separator if needed.

Parameters:

  • variant_file (str) – Path to the VCF file from which fields should be extracted.

  • fields (str) – A space-separated list of fields to extract (e.g. “CHROM POS REF ALT DP AD”).

  • cfg (dict) –

    Configuration dictionary that may include tool paths, parameters, etc.

    • ”extract_fields_separator”: str

      The separator for multi-sample fields when using SnpSift -s …. Often a comma “,”. Defaults to “,” if not present.

    • ”debug_level”: str or None

      Optional debug level to control how much we log.

  • output_file (str) – Path to the final TSV file where extracted fields will be written.

Returns:

The same output_file path that now contains the extracted fields (TSV).

Return type:

str

Raises:

RuntimeError – If the field extraction command fails.