REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
1000 Genomes Project data, phase 3 version 5a	The 1000 Genomes Project (1000 Genomes Project Consortium 2015)	ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
1000 Genomes Project data, high coverage	New York Genome Center (Byrska-Bishop et al. 2021)	http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20190425_NYGC_GATK/
Altai Denisovan and Vindija Neanderthal genomes, and genome masks	Kay Prüfer (Prufer et al., 2017)	http://cdna.eva.mpg.de/neandertal/Vindija/VCF/Vindija33.19/ http://cdna.eva.mpg.de/neandertal/Vindija/FilterBed/Vindija33.19/ http://cdna.eva.mpg.de/neandertal/Vindija/VCF/Denisova/ http://cdna.eva.mpg.de/neandertal/Vindija/FilterBed/Denisova/
HapMap genetic map	The International HapMap Consortium (The International HapMap Consortium 2007)	http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/
Software and algorithms
SPrime	Brian Browning (Browning et al. 2018)	https://github.com/browning-lab/sprime
Bcftools	SAMtools	http://samtools.github.io/bcftools/bcftools.html
SPrime pipeline	This protocol	https://github.com/YingZhou001/sprimepipeline
R	R Project (R Core Team 2019)	https://www.r-project.org/