Allele frequency differentiation among ancestry components in 1000 Genomes Project

This repository contains results from applying the selscan tool from Ohana (Cheng et al., 2022) to genotype data from 2,504 unrelated individuals from the 1000 Genomes Project Phase 3 dataset. The matrix of ancestral component proportions per sample was inferred from pruned variants (n = 106,740) on chr21 and is provided in chr21_pruned_50_Q.matrix (see Methods of Yan et al., 2021) and the inferred matrix of allele frequencies for these variants is provided in chr21_pruned_50_F.matrix. The Q matrix is visualized in Figure 3A of Yan et al. (2021). The file samples.txt contains sample identifiers in the order necessary to interpret these previous files. Files named chr*_ohana_scan.tsv.gz contain the results of the selscan tool, where the focal ancestral component is recorded in the last column. The column "lle_ratio" records log likelihood ratios, quantifying the extent to which allele frequencies of individual variants are better explained by the genome-wide covariance matrix or by an alternative covariance matrix where allele frequencies are allowed to vary in one of each of eight ancestry components. Higher values reflect support for the latter model. References Cheng, J. Y., Stern, A. J., Racimo, F., & Nielsen, R. (2022). Detecting selection in multiple populations by modeling ancestral admixture components. Molecular biology and evolution, 39(1), msab294. Yan, S. M., Sherman, R. M., Taylor, D. J., Nair, D. R., Bortvin, A. N., Schatz, M. C., & McCoy, R. C. (2021). Local adaptation and archaic introgression shape global diversity at human structural variant loci. Elife, 10, e67615.