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数据与复现
BI
bio-variant-calling-structural-variant-calling
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Call structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations that are too large for standard SNV callers. Use when detecting structural variants from short-read data.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-calling-structural-variant-calling
- 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：configManta.py (Manta)，delly call，lumpyexpress/smoove call。
- Call structural variants ，面向 my WGS data" → Detect large genomic rearrangements (deletions，insertions，inversions，duplications，translocations) ，使用 split-read 、 discordant-pair evidence. CLI：configManta.py (Manta)，delly call，lumpyexpress/smoove call。
- configManta.py \ --bam sample.bam \ --referenceFasta reference.fa \ --runDir manta_run。
原始文档
SKILL.md 摘录
Somatic SV calling
configManta.py
--tumorBam tumor.bam
--normalBam normal.bam
--referenceFasta reference.fa
--runDir manta_somatic
manta_somatic/runWorkflow.py -j 8
WES mode (for exome data)
configManta.py
--bam sample.bam
--referenceFasta reference.fa
--exome \ # Use exome settings
--callRegions regions.bed.gz \ # Restrict to regions
--runDir manta_exome
RNA-seq mode
configManta.py
--bam rnaseq.bam
--referenceFasta reference.fa
--rna \ # RNA-seq mode
--runDir manta_rna
适用场景
- 适合在detecting structural variants ，面向 short-read data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
- long-read-sequencing/structural-variants - Long-read SV calling
- copy-number/cnvkit-analysis - Copy number variants
- variant-calling/filtering-best-practices - Filter VCF files
- alignment-files/alignment-filtering - Prepare BAM files
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