SCI Skills

EN Index
Data & ReproClinical MedicineFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction
BI

bio-copy-number-cnv-annotation

Maintainer FreedomIntelligence · Last updated April 1, 2026

Annotate CNVs with genes, pathways, and clinical significance. Use when interpreting CNV calls or identifying affected genes from copy number analysis.

OpenClawNanoClawAnalysisReproductionbio-copy-number-cnv-annotation🧬 bioinformatics (gptomics bio-* suite)bioinformatics — clinical databases & variant analysisannotate

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-copy-number-cnv-annotation

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • CLI: bedtools intersect -a cnvs.bed -b genes.bed.
  • Python: pybedtools.BedTool().intersect().
  • 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().
  • awk 'NR>1 {print $1"\t"$2"\t"$3"\t"$5"\t"$6}' sample.cns > sample.cnv.bed.

Source Doc

Excerpt From SKILL.md

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 \
    --targets targets.bed \
    --annotate refFlat.txt \
    --fasta reference.fa \
    -o results/

Use cases

  • Use when interpreting CNV calls or identifying affected genes from copy number analysis.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • copy-number/cnvkit-analysis - Generate CNV calls
  • copy-number/cnv-visualization - Visualize annotated CNVs
  • pathway-analysis/go-enrichment - Enrichment of CNV genes
  • genome-intervals/bed-file-basics - BED file operations

Related skills

Related skills

Back to directory
AR
Data & ReproClinical Medicine

armored-cart-design-agent

Design armored CAR-T cells with cytokine payloads and resistance mechanisms.

OpenClawNanoClawAnalysis
FreedomIntelligence/OpenClaw-Medical-SkillsView
AR
Data & ReproClinical Medicine

arxiv-search

Search arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic search.

OpenClawNanoClawAnalysis
FreedomIntelligence/OpenClaw-Medical-SkillsView
AU
Data & ReproClinical Medicine

autonomous-oncology-agent

Autonomous oncology research agent: literature mining, trial matching, biomarker analysis, and treatment hypothesis generation.

OpenClawNanoClawAnalysis
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & ReproClinical Medicine

bio-cfdna-preprocessing

Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate remo…

OpenClawNanoClawAnalysis
FreedomIntelligence/OpenClaw-Medical-SkillsView