Samtools Bam Processor
Documentssamtools-bam-processorSamtools 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
QUICK START
How to use this skill
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Prompt to paste
Inspect the Agent Skill at https://github.com/a5c-ai/babysitter/blob/HEAD/library/specializations/domains/science/bioinformatics/skills/samtools-bam-processor/SKILL.md and all supporting files. Report provenance, permissions, scripts, dependencies, and security risks. Propose an exact installation into .agents/skills/samtools-bam-processor, but wait for my approval before writing files or running scripts.
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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)