{"doi":"10.1016/j.xgen.2022.100128","title":"Benchmarking challenging small variants with linked and long reads","abstract":"Genome in a Bottle benchmarks are widely used to help validate clinical sequencing pipelines and develop variant calling and sequencing methods. Here we use accurate linked and long reads to expand benchmarks in 7 samples to include difficult-to-map regions and segmental duplications that are challenging for short reads. These benchmarks add more than 300,000 SNVs and 50,000 insertions or deletions (indels) and include 16% more exonic variants, many in challenging, clinically relevant genes not covered previously, such as PMS2. For HG002, we include 92% of the autosomal GRCh38 assembly while excluding regions problematic for benchmarking small variants, such as copy number variants, that should not have been in the previous version, which included 85% of GRCh38. It identifies eight times more false negatives in a short read variant call set relative to our previous benchmark. We demonstrate that this benchmark reliably identifies false positives and false negatives across technologies, enabling ongoing methods development.","journal":"Cell Genomics","year":2022,"id":232368,"datarank":4.879513593380901,"base_score":5.3612921657094255,"endowment":5.3612921657094255,"self_citation_contribution":0.8041938248564139,"citation_network_contribution":4.075319768524487,"self_endowment_contribution":0.8041938248564139,"citer_contribution":4.075319768524487,"corpus_percentile":95.59062427477373,"corpus_rank":571,"citation_count":212,"citer_count":100,"citers_with_citation_signal":86,"citers_with_endowment":86,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.637,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":30899,"name":"Nathan D. 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Rosenfeld","orcid":"0000-0002-8750-2841","position":10,"is_corresponding":false},{"id":550913,"name":"Bohan Ni","orcid":"0000-0002-8570-6103","position":11,"is_corresponding":false},{"id":49044,"name":"Samantha Zarate","orcid":"0000-0001-5570-2059","position":12,"is_corresponding":false},{"id":49027,"name":"Melanie Kirsche","orcid":"0000-0002-6631-4761","position":13,"is_corresponding":false},{"id":49013,"name":"Sergey Aganezov","orcid":"0000-0003-2458-8323","position":14,"is_corresponding":false},{"id":24539,"name":"Michael C. Schatz","orcid":"0000-0002-4118-4446","position":15,"is_corresponding":false},{"id":391321,"name":"Giuseppe Narzisi","orcid":"0000-0003-1118-8849","position":16,"is_corresponding":false},{"id":550914,"name":"Marta Byrska-Bishop","orcid":"0000-0002-9118-1032","position":17,"is_corresponding":false},{"id":87011,"name":"Wayne E. Clarke","orcid":"0000-0003-2471-0712","position":18,"is_corresponding":false},{"id":62058,"name":"Uday S. 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