{"doi":"10.1093/gigascience/giaf154","title":"Challenges in structural variant calling in low-complexity regions","abstract":"<h4>Background</h4>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.<h4>Results</h4>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.<h4>Conclusion</h4>SVs are enriched and difficult to call in LCRs. Special care needs to be taken for calling and analyzing these variants.","journal":"GigaScience","year":2025,"id":2927,"datarank":0.3610996513646343,"base_score":1.791759469228055,"endowment":1.791759469228055,"self_citation_contribution":0.26876392038420827,"citation_network_contribution":0.092335730980426,"self_endowment_contribution":0.26876392038420827,"citer_contribution":0.092335730980426,"corpus_percentile":null,"corpus_rank":null,"citation_count":5,"citer_count":5,"citers_with_citation_signal":3,"citers_with_endowment":3,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.2289,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":30887,"name":"Alexandra P. Lewis","orcid":"0000-0002-6195-4786","position":1,"is_corresponding":false},{"id":23351,"name":"Qian Qin","orcid":"0000-0002-2119-6263","position":0,"is_corresponding":true}],"reference_count":38,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}