bio-duplicate-handling - Mark or remove PCR and optical duplicates
Marks or removes PCR and optical duplicates in BAM alignments with samtools fixmate and markdup, with assay-specific guidance on when duplicate handling is inappropriate.
Tags
Updated: 2026-10-01Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Mark PCR duplicates
- Remove duplicate reads
- Detect optical duplicates
- Validate assay compatibility
- Configure optical distance
- Use read-group boundaries
- Create BAM index
- Report duplicate statistics
Inputs
- Input BAM alignment
- Assay type
- Sequencing platform
- Read-group metadata
- Output paths
Outputs
- Marked or duplicate-removed BAM
- BAM index
- Duplicate statistics file
- Duplicate flags in BAM
Requirements
- samtools 1.19 or later
- pysam 0.22 or later for Python workflows