DougSpeed.com | The Home of LDAK (original) (raw)

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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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:

--> Using LDAK-KVIK to test SNPs and genes for association with a phenotype.

--> Using MegaPRS to construct polygenic scores from GWAS summary statistics.

--> 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.

If you are new to LDAK, I suggest you start by reading the Advice. If you have any problems, or spot any errors on this website, please contact me (see Help for details).
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Major updates:

February 2026. We have just released LDAK version 6.2, which contains new versions of MegaPRS and QuickPRS, that are faster, more accurate and easier to use.

December 2024. We have now released LDAK version 6.1, which contains an updated version of LDAK-KVIK, our new tool for mixed-model association analysis of quantitative and binary phenotypes. LDAK-KVIK is described in our paper LDAK-KVIK performs fast and powerful mixed-model association analysis of quantitative and binary phenotypes, published in Nature Genetics.

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.