Other Details

1000 Genomes Project data can be used for inferring ancestry.

Advanced Options explains how to set the working directory and random seed.

Data Filtering explains how to specify subsets of samples and/or predictors.

File Formats describes the many types of genetic data LDAK can accommodate.

High-LD Regions explains how to identify SNPs in regions of high linkage disequilibrium.

Kinship Formats explains how kinship matrices are saved.

Phenotypes and Covariates explains the format of phenotype and covariate files.

Quality Control provides guidelines for cleaning your data, and ways to check for inflation.

Reference Panel provides guidelines for constructing a reference panel.

Relatives Files are used to specify pairs of related individuals.

Sample Subsets can be provided with Haseman-Elston or PCGC Regression.

Summary Statistics explains how to format results from single-predictor analyses.