# Samtools Bam Processor

> Samtools Bam Processor is an Agent Skill for documents published in the a5c-ai/babysitter repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.

BAM/SAM file manipulation skill for sorting, indexing, filtering, and extracting alignment data

- Skill name: `samtools-bam-processor`
- Category: [Documents](https://www.openparable.com/skill/documents/1)
- Source: https://github.com/a5c-ai/babysitter/blob/HEAD/library/specializations/domains/science/bioinformatics/skills/samtools-bam-processor/SKILL.md
- Repository: a5c-ai/babysitter (1,548 GitHub stars when collected)

## SKILL.md

# 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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Source: https://www.openparable.com/skill/documents/samtools-bam-processor (OpenParable). Cite the canonical URL above.