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BI
bio-duplicate-handling
Maintainer FreedomIntelligence · Last updated April 1, 2026
Mark and remove PCR duplicates with Picard or samtools markdup.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-duplicate-handling
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Mark and remove PCR/optical duplicates using samtools.
- samtools sort -n -o namesort.bam input.bam.
Source Doc
Excerpt From SKILL.md
Why Remove Duplicates?
PCR duplicates are identical copies of the same original molecule, created during library preparation. They:
- Inflate coverage artificially
- Bias allele frequencies
- Can create false positive variant calls
Optical duplicates are clusters read multiple times due to their proximity on the flowcell.
Duplicate Marking Workflow
The standard samtools workflow requires multiple steps:
## 2. Add mate information with fixmate
samtools fixmate -m namesort.bam fixmate.bam
Use cases
- Use bio-duplicate-handling for genomics and bioinformatics workflows.
- Apply bio-duplicate-handling to sequencing, variant, or omics analysis tasks.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- alignment-sorting - Sort by name/coordinate for workflow
- alignment-filtering - Filter duplicates from output
- bam-statistics - Check duplicate rates with flagstat
- variant-calling - Duplicate marking before calling
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