bio-copy-number-cnv-annotation
Annotate CNVs with genes, pathways, and clinical significance. Use when interpreting CNV calls or identifying affected genes from copy number analysis.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-cnv-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: bedtools 2.31+, pandas 2.2+, pybedtools 0.9+, pysam 0.22+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters - 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. # CNV Annotation **"Annotate my CNV calls with gene names"** → Overlap CNV segments with gene annotations, clinical databases, and pathway information to identify affected genes and assess clinical significance. - CLI: `bedtools intersect -a cnvs.bed -b genes.bed` - Python: `pybedtools.BedTool().intersect()` ## Annotate with Gene Names (bedtools) ```bash # Convert CNV segments to BED awk 'NR>1 {print $1"\t"$2"\t"$3"\t"$5"\t"$6}' sample.cns > sample.cnv.bed # Intersect with gene annotations bedtools intersect -a sample.cnv.bed -b genes.bed -wa -wb > cnv_genes.txt # Get genes overlapping CNVs bedtools intersect -a genes.b
- Version Compatibility
- Annotate with Gene Names (bedtools)
- CNVkit Gene Annotation
- Python: Comprehensive Annotation
- Annotate with Cancer Gene Census
- Annotate with ACMG/ClinVar
- GISTIC2 for Recurrent CNVs
- AnnotSV for Comprehensive Annotation
- R: Gene Enrichment of CNV Regions
- Interpret CNV States
- Output Report
- Related Skills
Convert CNV segments to BED
awk 'NR>1 {print $1"\t"$2"\t"$3"\t"$5"\t"$6}' sample.cns > sample.cnv.bed
Intersect with gene annotations
bedtools intersect -a sample.cnv.bed -b genes.bed -wa -wb > cnv_genes.txt
Get genes overlapping CNVs
bedtools intersect -a genes.bed -b sample.cnv.bed -u > affected_genes.bed
Annotate during analysis
cnvkit.py batch tumor.bam --normal normal.bam \
Genes are included in output CNS file
Export segments for GISTICWhat does the bio-copy-number-cnv-annotation skill do?
Annotate CNVs with genes, pathways, and clinical significance. Use when interpreting CNV calls or identifying affected genes from copy number analysis.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-cnv-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.