LDAK

Thursday 6th November 2020. I have just updated the LDAK software to include the seven new Prediction tools, described in our preprint (currently available on Biorxiv). You can obtain the latest version of LDAK v5.1 from Downloads.

March 2020. Our most recent work, Evaluating and improving heritability models using summary statistics, has just been published in Nature Genetics (for a free version click here). This work represents a major update to SumHer, our tool for performing heritability analyses using summary statistics. In particular, it provides methods for comparing heritability models and for estimating theĀ selection-related parameter alpha.
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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:

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).