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)