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 BioTender-max/awesome-bio-agent-skills --skill 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 with bcftools Call SNPs and indels from aligned reads using bcftools mpileup/call. ## When to Use bcftools vs Other Callers | Scenario | Recommended Caller | Rationale | |----------|-------------------|-----------| | Quick exploratory analysis | bcftools | Fast, minimal setup, good accuracy for SNPs | | Non-model organisms | bcftools or FreeBayes | No training data required (unlike VQSR); adjustable ploidy | | Haploid/bacterial genomes | bcftools with `--ploidy 1` | Native ploidy support; simpler model appropriate for haploids | | Highest accuracy (human) | DeepVariant or GATK DRAGEN-mode | Deep learning or local assembly outperforms pileup-based calling | | Cohort joint genotyping | GATK (GVCF workflow) | bcftools multi-sample calling does not scale well beyond ~100 samples | | Somatic variants
- Version Compatibility
- When to Use bcftools vs Other Callers
- 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)
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 BioTender-max/awesome-bio-agent-skills --skill 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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.