This dataset includes ancient genotype data as described in Lipson, Sawchuk et al. (2022) in PACKEDANCESTRYMAP format.

You may convert the data to other formats using the "convertf" utility of EIGENSOFT (https://data.broadinstitute.org/alkesgroup/EIGENSOFT/).

A number of different analyses can be performed using the appliations in ADMIXTOOLS (https://github.com/DReichLab/AdmixTools).

The dataset includes three files: *.geno (genotype data), *.ind (individual data), and *.snp (SNP data). Together they contain genotype information for 21 ancient individuals from sub-Saharan Africa (six newly reported here). Individual I5950 (Mota, Ethiopia) is additionally represented in the dataset by whole-genome sequence data, with either one allele pulled down at random for each of the 1240k target sites (.SG suffix) or diploid genotype calls (.DG suffix). Complete WGS data files are available separately on the Reich lab website and on ENA (.fa and .bam, respectively; see below). Ten individuals have a second version provided here with an '_all' suffix, which indicates the inclusion of additional data from non-UDG-treated libraries.

BAM files:

You may find sequence read data for the individuals reported here in the European Nucleotide Archive (https://www.ebi.ac.uk/ena/) under accession number PRJEB49291.

Paper reference:

M. Lipson, E. A. Sawchuk, et al. "Ancient DNA and deep population structure in sub-Saharan African foragers." Nature (2022). 
