name: samtools-bam-processor description: BAM/SAM file manipulation skill for sorting, indexing, filtering, and extracting alignment data allowed-tools:

• Read
• Write
• Glob
• Grep
• Edit
• WebFetch
• WebSearch
• Bash metadata: version: "1.0" category: bioinformatics tags:
  • sequence-analysis
  • bam
  • sam
  • alignment

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)