A robust benchmark for detection of germline large deletions and insertions
Research output: Contribution to journal › Journal article › Research › peer-review
Detection of structural variants in the human genome is facilitated by a benchmark set of large deletions and insertions.
New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a sequence-resolved benchmark set for identification of both false-negative and false-positive germline large insertions and deletions. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle Consortium integrated 19 sequence-resolved variant calling methods from diverse technologies. The final benchmark set contains 12,745 isolated, sequence-resolved insertion (7,281) and deletion (5,464) calls >= 50 base pairs (bp). The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.51 Gbp and 5,262 insertions and 4,095 deletions supported by >= 1 diploid assembly. We demonstrate that the benchmark set reliably identifies false negatives and false positives in high-quality SV callsets from short-, linked- and long-read sequencing and optical mapping.
Original language | English |
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Journal | Nature Biotechnology |
Volume | 38 |
Issue number | 11 |
Pages (from-to) | 1347-+ |
Number of pages | 14 |
ISSN | 1087-0156 |
DOIs | |
Publication status | Published - Nov 2020 |
Externally published | Yes |
- STRUCTURAL VARIATION, HUMAN GENOME, VARIANTS, RESOURCE, SNP
Research areas
ID: 257032178