bio-vcf-manipulation
Merge, concatenate, sort, intersect, and subset VCF files using bcftools. Use when combining variant files, comparing call sets, or restructuring VCF data.
npx skills add BioTender-max/awesome-bio-agent-skills --skill vcf-manipulation --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: GATK 4.5+, bcftools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - 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. # VCF Manipulation Merge, concat, sort, and compare VCF files using bcftools. ## Operations Overview | Operation | Command | Use Case | |-----------|---------|----------| | Merge | `bcftools merge` | Combine samples from multiple VCFs | | Concat | `bcftools concat` | Combine regions from multiple VCFs | | Sort | `bcftools sort` | Sort unsorted VCF | | Intersect | `bcftools isec` | Compare/intersect call sets | | Subset | `bcftools view` | Extract samples or regions | ## Merge vs Concat Decision | Operation | Input structure | Result | Requires index | |-----------|----------------|--------|----------------| | `bcftools merge` | Different **samples** at (potentially) same positions | Multi-sample VCF | Yes | | `bcftools conc
- Version Compatibility
- Operations Overview
- Merge vs Concat Decision
- bcftools merge
- Basic Merge
- Merge Multiple Files
- Merge from File List
- Handle Missing Genotypes
- Force Sample Names
- Multiallelic Handling During Merge
- Merge Specific Regions
- bcftools concat
- Concatenate Chromosomes
- Concatenate All Chromosomes
bcftools merge sample1.vcf.gz sample2.vcf.gz -Oz -o merged.vcf.gz bcftools merge *.vcf.gz -Oz -o all_samples.vcf.gz bcftools merge -l files.txt -Oz -o merged.vcf.gz Output missing genotypes as ./. (default) Output missing as reference (0/0) bcftools merge --missing-to-ref sample1.vcf.gz sample2.vcf.gz -Oz -o merged.vcf.gz bcftools merge --force-samples sample1.vcf.gz sample2.vcf.gz -Oz -o merged.vcf.gz Keep SNPs and indels at same position as separate records bcftools merge --merge snps sample1.vcf.gz sample2.vcf.gz -Oz -o merged.vcf.gz No merging -- every record stays separate
What does the bio-vcf-manipulation skill do?
Merge, concatenate, sort, intersect, and subset VCF files using bcftools. Use when combining variant files, comparing call sets, or restructuring VCF data.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill vcf-manipulation --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.