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arXiv · 2509.23057

Challenges in structural variant calling in low-complexity regions

Qian Qin·Heng Li
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Abstract

Background: Structural variants (SVs) are genomic differences $\ge$50 bp in length. They remain challenging to detect even with long sequence reads, and the sources of these difficulties are not well quantified. Results: We identified 35.4 Mb of low-complexity regions (LCRs) in GRCh38. Although these regions cover only 1.2% of the genome, they contain 69.1% of confident SVs in sample HG002. Across long-read SV callers, 77.3-91.3% of erroneous SV calls occur within LCRs, with error rates increasing with LCR length. Conclusion: SVs are enriched and difficult to call in LCRs. Special care need to be taken for calling and analyzing these variants.

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Qian Qin, Heng Li. 2025-09-27. Challenges in structural variant calling in low-complexity regions. https://arxiv.org/abs/2509.23057

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