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PCR duplicate

Definition
AI-generated

PCR duplicates arise when library amplification copies the same original fragment multiple times; they appear as read pairs with identical or near-identical alignment coordinates.

Topics
Sequencing Data Analysis
Related
Duplicate read Optical duplicate

Why it matters in GWAS

PCR duplicates can dominate coverage in low-input libraries, so duplicate marking is standard before variant calling and depth-based QC.

Example usage

"PCR duplicate rates were higher in historical samples, motivating stricter depth filters."

Duplicate read Optical duplicate
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Picard toolkit: MarkDuplicates. Broad Institute.
← PCR amplification Peak calling →

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