Variant Fraction Tools

Configuration File: variant_fraction_tools.json Tool Type: Local Tools Count: 1

This page contains all tools defined in the variant_fraction_tools.json configuration file.

Available Tools

coding_variant_fraction (Type: CodingVariantFractionTool)

Compute the fraction of CODING variants in an Excel/CSV variant table that match a given Sequence…

coding_variant_fraction tool specification

Tool Information:

  • Name: coding_variant_fraction

  • Type: CodingVariantFractionTool

  • Description: Compute the fraction of CODING variants in an Excel/CSV variant table that match a given Sequence Ontology annotation and fall below a VAF threshold. Uses the CODING-only denominator convention (synonymous_variant, missense_variant, splice_region_variant, stop_gained, stop_lost, start_lost, frameshift_variant, inframe_insertion, inframe_deletion) - intronic, UTR, intergenic, and up/downstream records are excluded. Auto-detects ‘variant allele frequency’/’VAF’ and ‘Sequence Ontology’ columns if not specified. Supports flat headers (header_rows=1) and MultiIndex headers (header_rows=2) common in cancer variant reports. Returns the fraction with coding denominator plus the ‘naive’ fraction (over all VAF-filtered records) for comparison.

Parameters:

  • file (string) (required) Path to variant Excel (.xlsx) or CSV file.

  • vaf_threshold (number) (optional) Keep variants with VAF strictly less than this value. Default 0.3.

  • annotation (string) (optional) Sequence Ontology term to count in numerator. Default ‘synonymous_variant’.

  • header_rows (integer) (optional) 1 for flat headers, 2 for MultiIndex (common in Excel variant reports). Default 1.

  • vaf_col ([‘string’, ‘null’]) (optional) Explicit VAF column name. If empty, auto-detect from ‘variant allele freq’ or ‘vaf’.

  • so_col ([‘string’, ‘null’]) (optional) Explicit Sequence Ontology column name. If empty, auto-detect from ‘sequence ontology’.

Example Usage:

query = {
    "name": "coding_variant_fraction",
    "arguments": {
        "file": "example_value"
    }
}
result = tu.run(query)