KEY RESOURCES TABLE.

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
LASI-DAD Whole Genome Sequence	NIAGADS	https://dss.niagads.org/datasets ng00067
LASI-DAD Individual level summary statistics	NIAGADS	https://dss.niagads.org/datasets ng00171
1000 Genomes Whole Genome Sequence	IGSR	https://www.internationalgenome.org/data
Human Genome Diversity Project Whole Genome Sequence	IGSR	https://www.internationalgenome.org/data-portal/data-collection/hgdp
GenomeAsia Pilot project Whole Genome Sequence	European Genome Archive	EGAS00001002921
Allen Ancient DNA Resource	https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/FFIDCW	v54
RefSeq database	RefSeq	https://www.ncbi.nlm.nih.gov/refseq/
ClinVar database	ClinVar	https://www.ncbi.nlm.nih.gov/clinvar/; data release of 2023-12-17
Software and algorithms
BWA-mem	https://github.com/lh3/bwa	v0.7.15
BamUtil	https://genome.sph.umich.edu/wiki/BamUtil	v1.0.13
samtools	https://github.com/samtools/	version 1.12-25-g4eae367
samblaster	https://github.com/GregoryFaust/samblaster	version 0.1.24
sambamba	https://lomereiter.github.io/sambamba/	N/A
GATK	https://gatk.broadinstitute.org/hc/en-us/sections/360007336992-4-0-1-1	4.1.1
KING	https://www.kingrelatedness.com	v2.3.0
SHAPEIT	https://odelaneau.github.io/shapeit4/	4
liftOver	https://liftover.broadinstitute.org/	N/A
EIGENSOFT	https://github.com/DReichLab/EIG	v7.2.1
ADMIXTURE	https://dalexander.github.io/admixture/	v1.3.0
PLINK	https://www.cog-genomics.org/plink/2.0/	v2.00a2.3
ADMIXTOOLS	https://github.com/DReichLab/AdmixTools	v7.0.2
ALDER	https://cb.csail.mit.edu/alder/	v1.04
hap-IBD	https://github.com/browning-lab/hap-ibd	N/A
Variant Effect Predictor	https://github.com/Ensembl/ensembl-vep	version 105
LOFTEE	https://github.com/korradjk/loftee	v1.0.3
hmmix	https://github.com/LauritsSkov/Introgression-detection	version 1.0
GeneSCF	https://github.com/genescf/GeneSCF	N/A
BCF tools	https://samtools.github.io/bcftools/bcftools.html	v1.6
VCF tools	https://vcftools.github.io/index.html	0.1.16
R	https://www.r-project.org	version 4.4.0