Dataset	Reference	Link	Sample information (downloaded file format)
GIAB v3.3.2	(Zook et al., 2019)	https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv3.3.2/GRCh38/	Sample NA12878 (VCF and BED)
GIAB v4.2.1	(Wagner et al., 2022)	https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv4.2.1/GRCh38/	Sample NA12878 (VCF and BED)
GIAB genome stratification region files v2.0	(Krusche et al., 2019)	https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/genome-stratifications/v2.0/GRCh38/union/	NA (BED)
Platinum Genome	(Eberle et al., 2017)	https://www.illumina.com/platinumgenomes.html	Sample NA12878 (VCF)
1kGP phase 3	(The 1000 Genomes Project Consortium, 2015)	http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/	2,504 1kGP samples (VCF)
1kGP phase 3 GRCh38 SVs	(Sudmant et al., 2015)	http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/supporting/GRCh38_positions/	2,504 1kGP samples (VCF)
HGSVC	(Ebert et al., 2021)	http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/release/	34 1kGP samples and sample NA24385 (VCF)
SGDP	(Mallick et al., 2016)	https://www.ebi.ac.uk/ena/browser/view/PRJEB9586	110 SGDP samples listed in Table S7 (FastQ)