bio-vcf-statistics
Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck. Use when evaluating variant quality, comparing samples, or summarizing VCF contents.
npx skills add BioTender-max/awesome-bio-agent-skills --skill vcf-statistics --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 Statistics Generate statistics and quality metrics using bcftools. ## Statistics Tools | Command | Purpose | |---------|---------| | `bcftools stats` | Comprehensive variant statistics | | `bcftools gtcheck` | Sample concordance and relatedness | | `bcftools query` | Custom summaries | ## bcftools stats **Goal:** Generate comprehensive variant statistics including counts, Ti/Tv ratio, and quality distributions. **Approach:** Run bcftools stats and parse section-tagged output lines (SN, TSTV, AF, QUAL, DP). **"How many variants are in this VCF?"** → Compute summary counts, substitution types, and quality distributions from variant records. ### Basic Statistics ```bash bcftools stats input.vcf.gz > stats.txt ``` ### V
- Version Compatibility
- Statistics Tools
- bcftools stats
- Basic Statistics
- View Key Metrics
- Summary Numbers (SN)
- Transition/Transversion Ratio
- Per-Sample Statistics
- Compare Two VCFs
- Region-Specific Stats
- Plotting Statistics
- Generate Plots
- Comparison Plots
- Expected QC Metric Ranges
bcftools stats input.vcf.gz > stats.txt bcftools stats input.vcf.gz | grep "^SN" bcftools stats input.vcf.gz | grep "^SN" | cut -f3- bcftools stats input.vcf.gz | grep "^TSTV" bcftools stats -s - input.vcf.gz > per_sample.txt bcftools stats input1.vcf.gz input2.vcf.gz > comparison.txt bcftools stats -r chr1:1000000-2000000 input.vcf.gz > region_stats.txt bcftools stats -R exome.bed input.vcf.gz > exome_stats.txt plot-vcfstats -p output_dir stats.txt bcftools stats file1.vcf.gz file2.vcf.gz > comparison.txt
What does the bio-vcf-statistics skill do?
Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck. Use when evaluating variant quality, comparing samples, or summarizing VCF contents.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill vcf-statistics --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.