bio-variant-calling
Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-calling --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: bcftools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Variant Calling Call SNPs and indels from aligned reads using bcftools. ## Basic Workflow ``` BAM file + Reference FASTA | v bcftools mpileup (generate pileup) | v bcftools call (call variants) | v VCF file ``` ## 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. ### Basic Variant Calling ```bash bcftools mpileup -f reference.fa input.bam | bcftools call -mv -o variants.vcf ``` ### Output Compressed VCF ```bash bcftools mpileup -f reference.fa input.bam | bcftools call -mv -Oz -o variant
- Version Compatibility
- Basic Workflow
- bcftools mpileup + call
- Basic Variant Calling
- Output Compressed VCF
- Call Specific Region
- Call from Multiple BAMs
- BAM List File
- mpileup Options
- Quality Filtering
- Annotate with Read Depth
- Full Annotation Set
- Target Regions (BED)
- Max Depth
bcftools mpileup -f reference.fa input.bam | bcftools call -mv -o variants.vcf bcftools mpileup -f reference.fa input.bam | bcftools call -mv -Oz -o variants.vcf.gz bcftools index variants.vcf.gz bcftools mpileup -f reference.fa -r chr1:1000000-2000000 input.bam | \ bcftools call -mv -o region.vcf bcftools mpileup -f reference.fa sample1.bam sample2.bam sample3.bam | \ bcftools call -mv -o variants.vcf bcftools mpileup -f reference.fa -b bams.txt | bcftools call -mv -o variants.vcf bcftools mpileup -f reference.fa \ input.bam | bcftools call -mv -o variants.vcf
What does the bio-variant-calling skill do?
Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-calling --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.