alignment-level-QC

What problem does it solve?

This skill performs comprehensive alignment-level quality control for ChIP-seq and ATAC-seq BAM files, validating sorting, read groups, and overall mapping quality, and producing a MultiQC report to flag issues before downstream analyses.

Core Features & Use Cases

• Initialize the project directory structure under ${proj_dir} and prepare outputs.
• Check and fix BAM files by adding missing Read Groups, sorting, and indexing as needed.
• Run alignment QC metrics (flagstat, stats, insertsize, dup metrics) and generate a consolidated MultiQC report for per-sample quality assessment.

Quick Start

Run the alignment-level-QC workflow on a BAM file to generate per-sample QC metrics and a MultiQC report.