This dataset includes ancient genotype data as described in Lipson et al. (2018) 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 18 ancient individuals from Southeast Asia.  For nine individuals represented in two versions, the suffix "_all" refers to a merge that includes additional, non-UDG-treated libraries for that sample (not used for reported analyses; see paper for full details). The lab codes in the .ind file correspond to the sample codes given in the paper as follows (see also Table S1):

I0626	>	VN33
I0627	>	VN34
I10973	>	VN31
I1135	>	VN37
I1137	>	VN39
I1680	>	AB40
I1859	>	VN22
I2497	>	VN41
I2731	>	VN40
I2947	>	VN29
I2948	>	VN42
I4011	>	OAI1/S28
I4458	>	BCES B27
I7238	>	OAI1/S29 (same as lab code I4012)
I8970	>	BCES B16
I8974	>	BCES B38
I8977	>	BCES B54
I8978	>	BCES B67

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 PRJEB24939.

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

Paper reference:

M. Lipson et al. "Ancient genomes document multiple waves of migration in Southeast Asian prehistory." Science (2018). 
