LDAK

Hi, my name is Doug Speed, and I am a researcher at the Centre for Quantitative Genetics and Genomics at Aarhus University. However, enough about me! This website exists to host my software LDAK, and I hope you find some of it useful.
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March 2024. LDAK now includes TetraHer and QuantHer, methods for estimating family heritability for binary and quantitative traits. More details are provided in our paper Estimating disease heritability from complex pedigrees allowing for ascertainment and covariates, published in the American Journal of Human Genetics.

January 2023. We have added LDAK-GBAT, our new tool for gene-based association testing using GWAS summary statistics. Details of the tool can be found in our our paper LDAK-GBAT: fast and powerful gene-based association testing using summary statistics, published in the American Journal of Human Genetics, with scripts from the paper provided in Takiy's GitHub.
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LDAK is a software package for analysing association study data. In total, it has over 30 different functions (see Main Arguments for a full list). However, most likely, you will be interested in one of the following:

Testing predictors for association with a phenotype (either individually or jointly).

Estimating SNP heritability by analysing individual-level data

Estimating SNP heritability, heritability enrichments, genetic correlation and the selection-related parameter alpha by analysing summary statistics

Constructing SNP-based prediction models (polygenic risk scores)
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Central to LDAK is the Heritability Model, which describes the assumed distribution of heritability across the genome. In human genetics, it is common to assume that each SNP contributes equally. However, we have shown that it is better to use models where heritability depends on factors such as allele frequency and linkage disequilibrium (see Publications for more details).

If you are new to LDAK, I suggest you first obtain the latest version from Downloads, then read the Advice. If you have any problems, or spot any errors on this website, please contact me (see Help for details).