Challenges in structural variant calling in low-complexity regions
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arXiv
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| Format: | Preprint |
| Published: |
2025
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| _version_ | 1866911181203046400 |
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| author | Qin, Qian Li, Heng |
| author_facet | Qin, Qian Li, Heng |
| contents | 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. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2509_23057 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Challenges in structural variant calling in low-complexity regions Qin, Qian Li, Heng Genomics 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. |
| title | Challenges in structural variant calling in low-complexity regions |
| topic | Genomics |
| url | https://arxiv.org/abs/2509.23057 |