bio-vcf-basics
View, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting specific fields, or understanding VCF format structure.
npx skills add BioTender-max/awesome-bio-agent-skills --skill vcf-basics --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+, numpy 1.26+ 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/BCF Basics View and query variant files using bcftools and cyvcf2. ## Format Overview | Format | Description | Use Case | |--------|-------------|----------| | VCF | Text format, human-readable | Debugging, small files | | VCF.gz | Compressed VCF (bgzip) | Standard distribution | | BCF | Binary VCF | Fast processing, large files | ## VCF Format Structure ``` ##fileformat=VCFv4.2 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 chr1 1000 rs123 A G 30 PASS DP=50 GT:DP 0/1:25 ``` ### Header Lines (##) - `##fileformat` - VCF versi
- Version Compatibility
- Format Overview
- VCF Format Structure
- Header Lines (##)
- Column Header (#CHROM)
- Data Columns
- Critical Field Interpretation
- QUAL vs GQ: Different Questions
- AD vs DP Discrepancy
- Key INFO Annotations for Filtering
- PL (Phred-Scaled Likelihoods)
- bcftools view
- View VCF
- View Header Only
bcftools view input.vcf.gz | head bcftools view -h input.vcf.gz bcftools view -H input.vcf.gz | head bcftools view input.vcf.gz chr1:1000000-2000000 bcftools view -s sample1,sample2 input.vcf.gz bcftools view -s ^sample3 input.vcf.gz bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\n' input.vcf.gz bcftools query -f '%CHROM\t%POS\t%INFO/DP\t%INFO/AF\n' input.vcf.gz bcftools query -f '%CHROM\t%POS[\t%GT]\n' input.vcf.gz bcftools query -f '%CHROM\t%POS[\t%SAMPLE=%GT]\n' -s sample1,sample2 input.vcf.gz
What does the bio-vcf-basics skill do?
View, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting specific fields, or understanding VCF format structure.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill vcf-basics --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.