bio-variant-annotation
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance. Use when annotating variants with functional and clinical information.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-annotation --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: - 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. # Variant Annotation ## Tool Comparison | Tool | Best For | Speed | Output | |------|----------|-------|--------| | bcftools csq | Simple consequence prediction | Fast | VCF | | VEP | Comprehensive with plugins | Moderate | VCF/TXT | | SnpEff | Fast batch annotation | Fast | VCF | | ANNOVAR | Flexible databases | Moderate | TXT | ## bcftools annotate **Goal:** Add or remove INFO/ID annotations from external databases using bcftools. **Approach:** Match variants by position and allele against annotation VCF/BED/TAB files, copying specified columns. **"Add rsIDs to my VCF from dbSNP"** → Match variant positions against a database and copy identifiers or annotation fields into the VCF. ### Add Annotations from Database ```bash bcftools a
- Version Compatibility
- Tool Comparison
- bcftools annotate
- Add Annotations from Database
- Annotation Columns (-c)
- Add rsIDs from dbSNP
- Add Multiple Annotations
- Add from BED/TAB Files
- Remove Annotations
- Set ID from Fields
- bcftools csq
- Consequence Types
- Ensembl VEP
- Installation
bcftools annotate -a dbsnp.vcf.gz -c ID input.vcf.gz -Oz -o annotated.vcf.gz bcftools annotate -a dbsnp.vcf.gz -c ID input.vcf.gz -Oz -o with_rsids.vcf.gz bcftools annotate -a database.vcf.gz -c ID,INFO/AF,INFO/CAF input.vcf.gz -Oz -o annotated.vcf.gz BED with 4th column as annotation bcftools annotate -a regions.bed.gz -c CHROM,FROM,TO,INFO/REGION \ input.vcf.gz -Oz -o annotated.vcf.gz Tab file: CHROM POS VALUE bcftools annotate -a annotations.tab.gz -c CHROM,POS,INFO/SCORE \ bcftools annotate -x INFO/DP,INFO/MQ input.vcf.gz -Oz -o clean.vcf.gz bcftools annotate -x INFO input.vcf.gz -Oz -o minimal.vcf.gz # Remove all INFO
What does the bio-variant-annotation skill do?
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance. Use when annotating variants with functional and clinical information.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-annotation --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.