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)