AR
Design armored CAR-T cells with cytokine payloads and resistance mechanisms.
FreedomIntelligence/OpenClaw-Medical-Skills查看
数据与复现
BI
bio-copy-number-gatk-cnv
维护者 FreedomIntelligence · 最近更新 2026年4月1日
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.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-copy-number-gatk-cnv
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- CLI：gatk CollectReadCounts → gatk DenoiseReadCounts → gatk ModelSegments → gatk CallCopyRatioSegments。
- Call CNVs ，使用 GATK best practices" → Collect read counts，build panel of normals，denoise tumor coverage，model segments ，支持 allelic counts，、 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。
原始文档
SKILL.md 摘录
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.
适用场景
- 适合在following GATK best practices 或 integrating CNV calling ，支持 other GATK variant pipelines时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- 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
相关技能
相关技能
AR
数据与复现
arxiv-search
Search arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic sea…
FreedomIntelligence/OpenClaw-Medical-Skills查看
AU
Autonomous oncology research agent: literature mining, trial matching, biomarker analysis, and treatment hypothesis gene…
FreedomIntelligence/OpenClaw-Medical-Skills查看
BI
Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-…
FreedomIntelligence/OpenClaw-Medical-Skills查看