bio-duplicate-handling - Mark or remove PCR and optical duplicates
Marks or removes PCR and optical duplicates in BAM files with samtools fixmate and markdup for downstream analysis.
Tags
Updated: 2026-09-29Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Sort BAM alignments
- Add mate tags
- Mark duplicate reads
- Remove duplicate reads
- Index BAM files
- Count duplicate reads
Inputs
- Input BAM file
- Assay type
- Sequencing platform
- Read-group metadata
- Output file paths
Outputs
- Marked BAM file
- Deduplicated BAM file
- BAM index file
- Duplicate statistics file
Requirements
- samtools 1.19 or later
- Name-sorted BAM for fixmate
- Coordinate-sorted BAM for markdup