MarkDup
A fast, accurate BAM deduplication tool with intelligent UMI detection and correct fragment detection.
Why MarkDup?
MarkDup solves critical issues in BAM deduplication:
- Correct fragment detection: Proper strand-aware coordinate handling.
- High performance: Optimized algorithms and parallel processing.
- Smart UMI clustering: Frequency-aware algorithms to prevent over-merging.
- Automatic detection: Handles both UMI and non-UMI data seamlessly.
Quick Start
# Installation
pip install markdup
# Basic usage (auto-detects everything)
markdup -i input.bam -o output.bam
# With multiple threads
markdup -i input.bam -o output.bam --threads 8
# Force coordinate-based (no UMIs)
markdup -i input.bam -o output.bam --no-umi
Usage
For a full list of options and their descriptions, run:
markdup --help
Examples
Basic Deduplication
# Auto-detect UMIs and process
markdup -i input.bam -o output.bam
# Force coordinate-based method (no UMIs)
markdup -i input.bam -o output.bam --no-umi
Advanced Options
# Custom UMI settings
markdup -i input.bam -o output.bam --umi-tag UB --max-dist-frac 0.15
# Start-only positioning (useful for ChIP-seq)
markdup -i input.bam -o output.bam --start-only
# Keep duplicates and mark them
markdup -i input.bam -o output.bam --keep-duplicates
Output Format
MarkDup adds BAM tags to track deduplication:
| Tag | Description |
|---|---|
cn |
Cluster name (chr:start-end:strand:UMI) |
cs |
Cluster size (number of reads) |
Documentation
License
MIT License - see LICENSE for details.
Copyright © 2025-present Chang Y
1 maintainer
Metadata
1 maintainer
Release files for markdup 0.0.29
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