It combines a large, multi-platform long-read SV resource (HPRC, HGSVC, UW-ONT, IB-ONT) with rigorous multi-caller integration and demonstrates utility by identifying SV-disease associations in 230,000 All of Us participants.
This repository contains workflows and analysis scripts for creating a SV control set from 1725 1KG long-read genomes. These genomes are sequenced by HPRC (Lucas et al. Biorxiv 2026), HGSVC (Logsdon et al. Nature 2025), UW-ONT and IB-ONT.
The UW-ONT sequenced a total of 500 genomes, 400 are novel and 100 genomes were published by Gustafson et al. 2025. The IB-ONT genomes are published by Siegfried Schloissnig et.al. (Nature 2025). The SV control set has been used to identify potential pathogenic variants and new SV-disease associations in biobanks.
The table below lists the source of 1,218 genomes used to create the callset in Lin et al. Note that the number below counts for the unique genomes.
HG002 and HG005 are included as part of the HPRC dataset. We also included NA12877 and NA12878. NA12878 is also one of the genomes sequenced by GIAB and HGSVC. NA12877 is sequenced by IB-ONT but we used the assembly and data published in David Porubsky et al. Nature 2025
| Dataset | Genomes | Platform |
|---|---|---|
| HPRC | 232 | HiFi, UL-ONT |
| HGSVC | 61 | HiFi, UL-ONT |
| 1KG-ONT | 480 | ONT (R9, R10) |
| IB-ONT | 445 | ONT (R9) |
Multiple caller merged callset for each genome. Please check the index file (TBA) for download.
We provide both GRCh38 and T2T-CHM13 callsets (zenodo link, TBA) for 293 HPRC+HGSVC genomes and 1,218 genomes.
CHM13_INSDEL_HGSVC_HPRC_wAF.vcf.gz: Integrated SVs from HGSVC/HPRC genomes with estimated allele frequency.
CHM13_INSDEL_1218_wAF.vcf.gz: Integrated SVs from all dataset containing 1,218 genomes with estimated allele frequency.
GRCh38_INSDEL_HGSVC_HPRC_wAF.vcf.gz: Integrated SVs from HGSVC genomes with estimated allele frequency.
GRCh38_INSDEL_1218_wAF.vcf.gz: Integrated SVs from all dataset containing 1,218 genomes with estimated allele frequency.
The HPRC genomes are assembled with hifiasm and verkko. Please refer to HPRC [release](https://gith
The repository for 1KG long-read sequencing based SV discovery
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