# Samtools Bam Processor

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

- Skill: `a5c-ai/samtools-bam-processor` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/samtools-bam-processor`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/samtools-bam-processor/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/samtools-bam-processor

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# 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)