This repository contains the following subdirectories:

1. ldgms/ contains seven files for each LD block: a .snplist file, an LDGM, and five precision matrices.
*.snplist: the SNP list is table with one row per SNP, with columns: 
	index: these non-unique indices, starting at zero, correspond to rows and columns of the LDGMs. There can be multiple SNPs for a single index, which occurs when the corresponding mutations occur on the same brick of the bricked tree sequence. SNPs with the same index have high (nearly perfect) LD.
	site_ids: RSIDs of SNPs that have one
	anc_alleles: ancestral allele
	deriv_alleles: derived allele
	EUR: allele frequency of derived allele in EUR samples
	AFR: allele frequency of derived allele in AFR samples
	AMR: allele frequency of derived allele in AMR samples
	EAS: allele frequency of derived allele in EAS samples
	SAS: allele frequency of derived allele in SAS samples

*.edgelist: edge lists contain one row for each non-zero entry of the LDGM adjacency matrix or precision matrix. There is one LDGM edge list for each LD block, and five precision matrices for each LD block (one for each of the five continental populations). Each row represents an edge, as a tuple (index_1, index_2, entry). For the LDGM adjacency matrices, the entry is the edge weight, where 0 represents a strong dependency and e.g. 6 represents a weak dependency. For the LDGM precision matrix, it is the precision matrix entry. There are no column names. Precision matrices are named with the corresponding population (e.g., ‘*.EUR.edgelist’), while the LDGM has no population name.

2. genos/ contains genotype matrices for the 40 LD blocks on chromosomes 21-22, as number-of-SNPs by number-of-samples 0/1 matrices. Each LD matrix contains one column for each row in the SNP list files, and one row for each row in the sample ID files. It also contains a .csv file with the sample IDs and ancestry labels corresponding to each row of the .genos files.

3. ukb/ contains correlation matrices and SNP lists from UK Biobank data for chromosomes 21-22

4. sumstats/ contains four summary statistics files obtained from https://alkesgroup.broadinstitute.org/UKBB/