bam-toolkit
CommunityAnalyze BAMs: extract reads, indels, and coverage.
Authordakesan
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill helps you analyze BAM/SAM/CRAM alignment files from WGS/WES, including region-based read extraction, indel detection, and coverage statistics, with structured JSON outputs for downstream analysis.
Core Features & Use Cases
- Read Extraction: Pull reads from specific genomic regions.
- Indel Detection: Identify insertions and deletions from reads.
- Coverage Calculation: Compute coverage statistics for regions.
- JSON Export: Output results in JSON for easy integration.
Quick Start
Extract reads in chr1:1000-2000 as JSON, or compute coverage for the same region.
Dependency Matrix
Required Modules
pysamtyper
Components
scriptsreferences
💻 Claude Code Installation
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Please help me install this Skill: Name: bam-toolkit Download link: https://github.com/dakesan/cc-dnawork-plugin/archive/main.zip#bam-toolkit Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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