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Duplicate marking

Definition
AI-generated

Duplicate marking is the step in a sequencing pipeline that labels read pairs (or reads) as duplicates—typically PCR or optical duplicates—so downstream steps such as variant calling treat them as a single observation of the same DNA fragment.

Topics
Sequencing Data Analysis
Related
Duplicate read Genome Analysis Toolkit (GATK) Optical duplicate

Why it matters in GWAS

Duplicate marking reduces inflated read support at sites and stabilizes depth-based QC; omitting it can bias allele-balance and variant-quality statistics used before association testing.

Example usage

"Duplicate marking was performed with Picard MarkDuplicates; marked duplicates were excluded from variant discovery."

Duplicate read Genome Analysis Toolkit (GATK) Optical duplicate PCR duplicate Picard
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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