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bio-variant-calling
Maintainer FreedomIntelligence · Last updated April 1, 2026
Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-calling
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
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
bcftools mpileup + call
Goal: Detect SNPs and indels from aligned reads using the bcftools pileup-and-call pipeline.
Approach: Generate per-position pileup likelihoods with mpileup, then call genotypes with the multiallelic caller.
"Call variants from my BAM file" → Generate genotype likelihoods from aligned reads and identify variant sites using a Bayesian caller.
mpileup Options
Goal: Control pileup generation with quality thresholds, annotations, and region restrictions.
Approach: Set minimum mapping/base quality, request specific FORMAT/INFO tags, and restrict to target regions.
Calling Models
| Flag | Model | Use Case |
|---|---|---|
-m | Multiallelic caller | Default, recommended |
-c | Consensus caller | Legacy, single sample |
Use cases
- Use when detecting variants from BAM files or generating VCF from alignments.
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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