bio-copy-number-gatk-cnv
Call copy number variants using GATK best practices workflow. Supports both somatic (tumor-normal) and germline CNV detection from WGS or WES data. Use when following GATK best practices or integrating CNV calling with other GATK variant pipelines.
npx skills add majiayu000/claude-skill-registry --skill gatk-cnv-gptomics-bioskills-2 --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.
# GATK CNV Workflow ## Somatic CNV Workflow Overview ``` 1. PreprocessIntervals → intervals.interval_list 2. CollectReadCounts → sample.counts.hdf5 3. CreateReadCountPanelOfNormals → pon.hdf5 4. DenoiseReadCounts → sample.denoised.tsv 5. CollectAllelicCounts → sample.allelicCounts.tsv 6. ModelSegments → sample.modelFinal.seg 7. CallCopyRatioSegments → sample.called.seg ``` ## Step 1: Preprocess Intervals ```bash # For WES/targeted gatk PreprocessIntervals \ -R reference.fa \ -L targets.interval_list \ --bin-length 0 \ --interval-merging-rule OVERLAPPING_ONLY \ -O preprocessed.interval_list # For WGS gatk PreprocessIntervals \ -R reference.fa \ --bin-length 1000 \ --padding 0 \ -O wgs.interval_list ``` ## Step 2: Collect Read Counts ```bash # For each sample gatk CollectReadCounts \ -R reference.fa \ -I sample.bam \ -L preprocessed.interval_list \ --interval-merging-rule OVERLAPPING_ONLY \ -O sample.counts.hdf5 ``` ## Step 3: Create Panel of Normals ```bash # Combine multiple normal samples gatk CreateReadCountPanelOfNormals \ -I normal1.counts.hdf5 \ -I normal2.counts.hdf5 \ -I normal3.counts.hdf5 \ --minimum-interval-median-percentile 5.0 \ -O cnv_pon.hdf5 ``` ## Step 4: Denoise R
- Somatic CNV Workflow Overview
- Step 1: Preprocess Intervals
- Step 2: Collect Read Counts
- Step 3: Create Panel of Normals
- Step 4: Denoise Read Counts
- Step 5: Collect Allelic Counts
- Step 6: Model Segments
- Step 7: Call Copy Ratio Segments
- Plotting
- Germline CNV Workflow
- Complete Somatic Pipeline Script
- Key Output Files
- Related Skills
For WES/targeted gatk PreprocessIntervals \ For WGS For each sample gatk CollectReadCounts \ Combine multiple normal samples gatk CreateReadCountPanelOfNormals \ Using panel of normals gatk DenoiseReadCounts \ From known SNP sites (for LOH detection)
What does the bio-copy-number-gatk-cnv skill do?
Call copy number variants using GATK best practices workflow. Supports both somatic (tumor-normal) and germline CNV detection from WGS or WES data. Use when following GATK best practices or integrating CNV calling with other GATK variant pipelines.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill gatk-cnv-gptomics-bioskills-2 --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 majiayu000/claude-skill-registry, a repository with 534 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.