Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

variant-calling

Maintainer FreedomIntelligence · Last updated April 1, 2026

variant-calling.

OpenClawNanoClawAnalysisReproductionvariant-callingopenclaw medical skillsadditional scientific toolsvariant

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Call SNPs and indels from aligned reads using bcftools.
bcftools mpileup -f reference.fa -b bams.txt | bcftools call -mv -o variants.vcf.

Source Doc

Excerpt From SKILL.md

Calling Models

Flag	Model	Use Case
`-m`	Multiallelic caller	Default, recommended
`-c`	Consensus caller	Legacy, single sample

Output Variants Only

bcftools mpileup -f reference.fa input.bam | bcftools call -mv -o variants.vcf

## Output All Sites

```bash
bcftools mpileup -f reference.fa input.bam | bcftools call -m -o all_sites.vcf

Use cases

Use variant-calling for genomics and bioinformatics workflows.
Apply variant-calling to sequencing, variant, or omics analysis tasks.

Not for

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

Upstream Related Skills

vcf-basics - View and query resulting VCF
filtering-best-practices - Filter variants by quality
variant-normalization - Normalize indels
alignment-files/pileup-generation - Alternative pileup generation

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