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

vcf-statistics

Maintainer FreedomIntelligence · Last updated April 1, 2026

vcf-statistics.

OpenClawNanoClawAnalysisReproductionvcf-statisticsopenclaw medical skillsadditional scientific toolsvcf

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

Summary Numbers (SN)

Reports:

Number of samples
Number of records
Number of SNPs
Number of indels
Number of multiallelic sites
Number of multiallelic SNPs

Use cases

Use vcf-statistics for statistical testing and quantitative analysis.
Apply vcf-statistics to research datasets that require rigorous inference.

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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