Data & ReproStatistics & Data AnalysisFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-vcf-statistics

Maintainer FreedomIntelligence · Last updated April 1, 2026

Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck. Use when evaluating variant quality, comparing samples, or summarizing VCF contents.

OpenClawNanoClawAnalysisReproductionbio-vcf-statistics🧬 bioinformatics (gptomics bio-* suite)bioinformatics — clinical databases & variant analysisgenerate

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-vcf-statistics

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Generate statistics and quality metrics using bcftools.
bcftools view -v snps -H input.vcf.gz | wc -l.

Source Doc

Excerpt From SKILL.md

Statistics Tools

Command	Purpose
`bcftools stats`	Comprehensive variant statistics
`bcftools gtcheck`	Sample concordance and relatedness
`bcftools query`	Custom summaries

bcftools stats

Goal: Generate comprehensive variant statistics including counts, Ti/Tv ratio, and quality distributions.

Approach: Run bcftools stats and parse section-tagged output lines (SN, TSTV, AF, QUAL, DP).

"How many variants are in this VCF?" → Compute summary counts, substitution types, and quality distributions from variant records.

View Key Metrics

Output sections:

SN - Summary numbers
TSTV - Transitions/transversions
SiS - Singleton stats
AF - Allele frequency distribution
QUAL - Quality distribution
IDD - Indel distribution
ST - Substitution types
DP - Depth distribution

Use cases

Use when evaluating variant quality, comparing samples, or summarizing VCF contents.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

vcf-basics - View and query VCF files
filtering-best-practices - Evaluate filter impact
vcf-manipulation - Compare call sets
variant-calling - Assess calling quality

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