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Decoy sequence

Definition
AI-generated

Decoy sequences are extra reference entries (for example hs38d) that absorb reads from paralogous or viral sequence to reduce mismapping to the primary assembly.

Topics
Sequencing Data Analysis
Related
Alternate contig Reference genome

Why it matters in GWAS

Including decoys in the alignment reference lowers false variant calls caused by reads misplaced from repetitive homology.

Example usage

"The hs38 decoy sequence FASTA was included in the BWA index to match gnomAD mapping."

Alternate contig Reference genome
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

  • Li H. (2014). Toward better understanding of artifacts in variant calling. bioRxiv.
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