samtools-bam-processor

# 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)