This dataset includes ancient genotype data as described in Lipson et al. (2020) 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 the four ancient individuals from Shum Laka (Cameroon). Individuals I10871 and I10873 are additionally represented in the dataset by whole-genome sequence data, with one allele pulled down at random for each of the 1240k target sites (Shum_Laka.SG), and I10871 as well by diploid genotype calls from the whole-genome sequence data (Shum_Laka.DG). Complete WGS results for those two individuals are available separately on the Reich lab website.

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 PRJEB32086.

For questions and issues regarding this dataset, please contact Mark Lipson (mlipson[at]genetics.med.harvard.edu).

Paper reference:

M. Lipson et al. "Ancient West African foragers in the context of African population history." Nature (2020). 
