Vcf Stats Tools

Configuration File: vcf_stats_tools.json Tool Type: Local Tools Count: 3

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

Available Tools

VCF_count_variants (Type: VCFStatsTool)

Count variants in a local VCF/BCF after applying filters, via bcftools. Returns total records plu…

VCF_count_variants tool specification

Tool Information:

  • Name: VCF_count_variants

  • Type: VCFStatsTool

  • Description: Count variants in a local VCF/BCF after applying filters, via bcftools. Returns total records plus SNP/indel/MNP breakdown. Supports PASS-only, region, min QUAL, and a custom bcftools include expression so SNP/indel counts under a filter are deterministic. Requires bcftools on PATH.

Parameters:

  • operation (unknown) (required) Operation (fixed)

  • vcf_path (string) (required) Path to a local .vcf, .vcf.gz, or .bcf file

  • pass_only ([‘boolean’, ‘null’]) (optional) If true, count only FILTER=PASS or ‘.’ records

  • regions ([‘string’, ‘null’]) (optional) Restrict to a region, e.g. ‘chr1’ or ‘chr1:1-1000000’

  • min_qual ([‘number’, ‘null’]) (optional) Keep only records with QUAL >= this value

  • include_expr ([‘string’, ‘null’]) (optional) Extra bcftools -i include expression, e.g. ‘INFO/AF>0.01’

Example Usage:

query = {
    "name": "VCF_count_variants",
    "arguments": {
        "operation": "example_value",
        "vcf_path": "example_value"
    }
}
result = tu.run(query)

VCF_normalize (Type: VCFStatsTool)

Normalize a local VCF/BCF with bcftools norm (split or join multiallelics; left-align indels agai…

VCF_normalize tool specification

Tool Information:

  • Name: VCF_normalize

  • Type: VCFStatsTool

  • Description: Normalize a local VCF/BCF with bcftools norm (split or join multiallelics; left-align indels against a reference FASTA when given) and report SNP/indel/record counts before vs after. Resolves the common cause of disagreeing indel counts: un-split multiallelics and non-left-aligned indels. Requires bcftools on PATH.

Parameters:

  • operation (unknown) (required) Operation (fixed)

  • vcf_path (string) (required) Path to a local .vcf, .vcf.gz, or .bcf file

  • multiallelics ([‘string’, ‘null’]) (optional) ‘split’ (default) breaks multiallelic records into biallelic; ‘join’ merges; ‘none’ leaves as-is

  • reference_fasta ([‘string’, ‘null’]) (optional) Optional reference FASTA path; enables indel left-alignment (-f)

Example Usage:

query = {
    "name": "VCF_normalize",
    "arguments": {
        "operation": "example_value",
        "vcf_path": "example_value"
    }
}
result = tu.run(query)

VCF_summary_stats (Type: VCFStatsTool)

Canonical variant statistics for a local VCF/BCF file via bcftools stats. Returns records, SNPs, …

VCF_summary_stats tool specification

Tool Information:

  • Name: VCF_summary_stats

  • Type: VCFStatsTool

  • Description: Canonical variant statistics for a local VCF/BCF file via bcftools stats. Returns records, SNPs, indels, MNPs, multiallelic sites, ts/tv ratio, and per-sample het/hom/missing counts. Optional PASS-only, region, QUAL, and bcftools-expression filters. Use this instead of writing an ad-hoc parser so counts are reproducible. Requires bcftools on PATH.

Parameters:

  • operation (unknown) (required) Operation (fixed)

  • vcf_path (string) (required) Path to a local .vcf, .vcf.gz, or .bcf file

  • pass_only ([‘boolean’, ‘null’]) (optional) If true, count only FILTER=PASS or ‘.’ records

  • regions ([‘string’, ‘null’]) (optional) Restrict to a region, e.g. ‘chr1’ or ‘chr1:1-1000000’ (streamed, no index needed)

  • min_qual ([‘number’, ‘null’]) (optional) Keep only records with QUAL >= this value

  • include_expr ([‘string’, ‘null’]) (optional) Extra bcftools -i include expression, e.g. ‘INFO/DP>10’

Example Usage:

query = {
    "name": "VCF_summary_stats",
    "arguments": {
        "operation": "example_value",
        "vcf_path": "example_value"
    }
}
result = tu.run(query)