Year: 2025
Type: preprint
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.
Source: arXiv (Cornell University)
Authors: Qin, Qian, Li, Heng
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7084165012
Cites:
Cited by:
Related to: