Data & ReproClinical MedicineFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-vcf-basics

Maintainer FreedomIntelligence · Last updated April 1, 2026

View, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting specific fields, or understanding VCF format structure.

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

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

View and query variant files using bcftools and cyvcf2.
bcftools index -t input.vcf.gz.

Source Doc

Excerpt From SKILL.md

Format Overview

Format	Description	Use Case
VCF	Text format, human-readable	Debugging, small files
VCF.gz	Compressed VCF (bgzip)	Standard distribution
BCF	Binary VCF	Fast processing, large files

Header Lines (##)

##fileformat - VCF version
##INFO - INFO field definitions
##FORMAT - FORMAT field definitions
##FILTER - Filter definitions
##contig - Reference contigs
##reference - Reference genome

Column Header (#CHROM)

Fixed columns: CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT Followed by sample columns

Use cases

Use when inspecting variants, extracting specific fields, or understanding VCF format structure.

Not for

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

Upstream Related Skills

variant-calling - Generate VCF from alignments
filtering-best-practices - Filter variants by quality/criteria
vcf-manipulation - Merge, concat, intersect VCFs
alignment-files/pileup-generation - Generate pileup for calling

Related skills

Back to directory

Data & ReproClinical Medicine

armored-cart-design-agent

Design armored CAR-T cells with cytokine payloads and resistance mechanisms.

OpenClawNanoClawAnalysis

FreedomIntelligence/OpenClaw-Medical-SkillsView

Data & ReproClinical Medicine

arxiv-search

Search arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic search.

OpenClawNanoClawAnalysis

FreedomIntelligence/OpenClaw-Medical-SkillsView

Data & ReproClinical Medicine

autonomous-oncology-agent

Autonomous oncology research agent: literature mining, trial matching, biomarker analysis, and treatment hypothesis generation.

OpenClawNanoClawAnalysis

FreedomIntelligence/OpenClaw-Medical-SkillsView

Data & ReproClinical Medicine

bio-cfdna-preprocessing

Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate remo…

OpenClawNanoClawAnalysis

FreedomIntelligence/OpenClaw-Medical-SkillsView