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bio-copy-number-gatk-cnv
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-copy-number-gatk-cnv
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: gatk CollectReadCounts → gatk DenoiseReadCounts → gatk ModelSegments → gatk CallCopyRatioSegments.
- Call CNVs using GATK best practices" → Collect read counts, build a panel of normals, denoise tumor coverage, model segments with allelic counts, and call copy ratio states. CLI: gatk CollectReadCounts → gatk DenoiseReadCounts → gatk ModelSegments → gatk CallCopyRatioSegments.
- gatk PreprocessIntervals \ -R reference.fa \ -L targets.interval_list \ --bin-length 0 \ --interval-merging-rule OVERLAPPING_ONLY \ -O preprocessed.interval_list.
Source Doc
Excerpt From SKILL.md
Step 1: Preprocess Intervals
Goal: Prepare genomic intervals for read counting, handling both WES and WGS modes.
Approach: Use PreprocessIntervals to bin or merge target intervals with appropriate padding.
## For WGS
gatk PreprocessIntervals \
-R reference.fa \
--bin-length 1000 \
--padding 0 \
-O wgs.interval_list
Step 2: Collect Read Counts
Goal: Count reads per interval for each sample.
Approach: Run CollectReadCounts on each BAM against the preprocessed intervals.
Use cases
- Use when following GATK best practices or integrating CNV calling with other GATK variant pipelines.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- copy-number/cnvkit-analysis - Alternative CNV caller
- copy-number/cnv-visualization - Plotting results
- alignment-files/bam-statistics - Input BAM QC
- variant-calling/variant-calling - SNP calling for allelic counts
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