BAM-filtration

What problem does it solve?

Cleans raw BAM files by removing artifacts such as mitochondrial reads, blacklist regions, PCR duplicates, and unmapped reads to produce a clean BAM ready for peak calling.

Core Features & Use Cases

• Detects BAM inputs that are coordinate-sorted and contain read groups and filters artifacts to produce cleaned outputs per sample.
• Optionally prompts for blacklist usage if blacklist file is missing, and applies blacklist filtering when provided.
• Initializes a project directory structure and organizes outputs under a per-sample filtered_bam folder, including temporary data as needed.
• Outputs cleaned BAMs (sample.filtered.bam) and indices (sample.filtered.bam.bai), suitable for QC and downstream peak calling workflows.

Quick Start

Place your raw BAMs in the working directory and run the skill to generate cleaned BAMs in the project output folder.