samtools-bam-processor

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"]}
graph	{"domains":["domain:bioinformatics"],"specializations":["specialization:biomedical-informatics"],"skillAreas":["skill-area:python-data-pipelines","skill-area:data-analysis","skill-area:graph-algorithms"],"workflows":["workflow:experiment-design"],"roles":["role:research-engineer","role:lab-technician"]}

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)