{"doi":"10.1126/science.abg8871","title":"Pangenomics enables genotyping of known structural variants in 5202 diverse genomes","abstract":"We introduce Giraffe, a pangenome short-read mapper that can efficiently map to a collection of haplotypes threaded through a sequence graph. Giraffe maps sequencing reads to thousands of human genomes at a speed comparable to that of standard methods mapping to a single reference genome. The increased mapping accuracy enables downstream improvements in genome-wide genotyping pipelines for both small variants and larger structural variants. We used Giraffe to genotype 167,000 structural variants, discovered in long-read studies, in 5202 diverse human genomes that were sequenced using short reads. We conclude that pangenomics facilitates a more comprehensive characterization of variation and, as a result, has the potential to improve many genomic analyses.","journal":"Science","year":2021,"id":145443,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":419,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9529,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":6315,"name":"Jean Monlong","orcid":"0000-0002-9737-5516","position":1,"is_corresponding":false},{"id":231855,"name":"Xian Chang","orcid":"0000-0002-3801-4542","position":2,"is_corresponding":false},{"id":109821,"name":"Adam M. Novak","orcid":"0000-0001-5828-047X","position":3,"is_corresponding":false},{"id":6318,"name":"Jordan M. Eizenga","orcid":"0000-0001-8345-8356","position":4,"is_corresponding":false},{"id":280976,"name":"Charles Markello","orcid":"0000-0002-3653-7155","position":5,"is_corresponding":false},{"id":30906,"name":"Jonas A. Sibbesen","orcid":"0000-0002-5528-0236","position":6,"is_corresponding":false},{"id":6314,"name":"Hickey, Glenn","orcid":"0000-0002-2280-9404","position":7,"is_corresponding":false},{"id":24447,"name":"Pi-Chuan Chang","orcid":"0000-0003-3021-6446","position":8,"is_corresponding":false},{"id":227319,"name":"Andrew Carroll","orcid":"0000-0002-4824-6689","position":9,"is_corresponding":false},{"id":1010,"name":"Namrata Gupta","orcid":"0000-0001-6786-4995","position":10,"is_corresponding":false},{"id":226943,"name":"Stacey Gabriel","orcid":"0000-0001-6939-2215","position":11,"is_corresponding":false},{"id":16070,"name":"Thomas W. Blackwell","orcid":"0000-0001-9437-1176","position":12,"is_corresponding":false},{"id":19559,"name":"Aakrosh Ratan","orcid":"0000-0002-0782-3056","position":13,"is_corresponding":false},{"id":236910,"name":"Kent D. Taylor","orcid":"0000-0002-2756-4370","position":14,"is_corresponding":false},{"id":11274,"name":"Stephen S. Rich","orcid":"0000-0003-3872-7793","position":15,"is_corresponding":false},{"id":11276,"name":"Jerome I. Rotter","orcid":"0000-0001-7191-1723","position":16,"is_corresponding":false},{"id":109463,"name":"David Haussler","orcid":"0000-0003-1533-4575","position":17,"is_corresponding":false},{"id":109462,"name":"Erik Garrison","orcid":"0000-0003-3821-631X","position":18,"is_corresponding":false},{"id":108063,"name":"Benedict Paten","orcid":"0000-0001-8863-3539","position":19,"is_corresponding":false},{"id":24549,"name":"Jouni Sirén","orcid":"0000-0001-5828-4139","position":0,"is_corresponding":true}],"reference_count":69,"raw_metadata":null,"created_at":"2026-07-18T23:42:12.871665Z","pmid":"34914532","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":[]}