replicates-incorporation

What problem does it solve?

This skill ensures reproducible peak analyses by systematically merging BAM files and, when needed, creating pseudo-replicates to enable stable downstream peak calling and consensus formation.

Core Features & Use Cases

• Supports pre-peak calling (BAM mode) by pooling BAMs and optionally splitting into two balanced pseudo-replicates.
• Supports post-peak calling (Peak mode) by performing IDR analysis to derive a conservative or optimal consensus peak set.
• Ideal for experiments with multiple replicates who require deterministic, reproducible peak lists and clear output structure.

Quick Start

Run the replicates-incorporation workflow to merge BAMs and, if requested, generate two pseudo-replicates for peak calling.