ReddRadar
Agent skill
samtools-bam-processor
BAM/SAM file manipulation skill for sorting, indexing, filtering, and extracting alignment data
Install this agent skill to your Project
npx add-skill https://github.com/a5c-ai/babysitter/tree/main/library/specializations/domains/science/bioinformatics/skills/samtools-bam-processor
Metadata
Additional technical details for this skill
- tags
-
sequence-analysis bam sam alignment
- version
- 1.0
- category
- bioinformatics
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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