samtools-bam-processor
BAM/SAM file manipulation skill for sorting, indexing, filtering, and extracting alignment data
Best use case
samtools-bam-processor is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
BAM/SAM file manipulation skill for sorting, indexing, filtering, and extracting alignment data
Teams using samtools-bam-processor should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/samtools-bam-processor/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How samtools-bam-processor Compares
| Feature / Agent | samtools-bam-processor | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
BAM/SAM file manipulation skill for sorting, indexing, filtering, and extracting alignment data
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
SKILL.md Source
# Samtools BAM Processor Skill ## Purpose Provide BAM/SAM file manipulation capabilities for sorting, indexing, filtering, and extracting alignment data. ## Capabilities - BAM sorting and indexing - Duplicate marking and removal - Alignment statistics generation - Region extraction and filtering - Read group management - Format conversion (SAM/BAM/CRAM) ## Usage Guidelines - Sort and index BAM files for efficient access - Mark or remove duplicates based on protocol - Generate alignment statistics for quality assessment - Extract regions of interest for targeted analysis - Manage read groups for multi-sample data - Use CRAM for storage efficiency ## Dependencies - samtools - Picard - sambamba ## Process Integration - Whole Genome Sequencing Pipeline (wgs-analysis-pipeline) - Tumor Molecular Profiling (tumor-molecular-profiling) - RNA-seq Differential Expression Analysis (rnaseq-differential-expression)
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