Samtools BAM Processor Skill

SkillFiles & storage

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

Instructions available. Your AI can read the instructions. Execution depends on the setup they require.

Account requirements not reviewed. Check the skill instructions before use; ahel provides instructions and does not run this skill.

Add ahel to your AI once: Claude, ChatGPT, Cursor, Claude Code or Codex. Then ask it to use this.

Then ask your AI: use the Samtools BAM Processor Skill skill

What this skill tells your AI

The instructions your AI receives, as published by a5c-ai/babysitter in library/specializations/domains/science/bioinformatics/skills/samtools-bam-processor/SKILL.md and read by ahel’s review.

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)

Signals

GitHub stars: 2k
Forks: 112
Last commit: Sep 2026

Advanced

Item type: skill
Key: samtools-bam-processor
Source: github.com/a5c-ai/babysitter

github.com/a5c-ai/babysitter