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Duplicate read

Definition
AI-generated

Duplicate reads are extra copies of the same DNA fragment arising from PCR or optical clustering; pipelines mark duplicates so downstream callers do not overweight the same molecule.

Topics
Sequencing Data Analysis
Related
Duplicate marking Optical duplicate PCR duplicate

Why it matters in GWAS

Failure to mark duplicates inflates apparent support for variants and distorts allele balance metrics used in QC.

Example usage

"Picard marked each duplicate read; optical duplicates were distinguished from PCR duplicates."

Duplicate marking Optical duplicate PCR duplicate Picard Read Depth
Related-term network

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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.
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