Introduction

We're in Nature Genetics again! Click here, or here, or here! (or for a free version, here)

LDAK 5 now out! - Click on Downloads

To accompany Version 5, we have written step-by-step guides for computing SNP heritability either using raw data or GWAS summary statistics.
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LDAK is back, and better than ever! Version 5 includes everything you need to perform the analyses in our latest publication; it does the following:

Calculates LDAK SNP weightings (now much quicker than before)
Computes weighted and unweighted kinship matrices
Generalised REML Solver - allows for both kinships and regions
Super-efficient mixed-model analysis
Gene-based Association Testing
MultiBLUP Prediction - it's the best!

Investigate genetic architecture from summary statistics using SumHer

Performs kinship matrix manipulation (add/subtracting/converting)
Calculation of BLUP effect size estimates
Haseman-Elston and PCGC Regression
Genetic risk scoring - allows for multiple profiles
Principal component analysis
Generates simulated genotypes and phenotypes
Can accommodate / convert to a wide-range of data formats

The original use of LDAK was to adjust for linkage disequilibrium (LD) by calculating SNP weightings which downweight the contribution of SNPs in highly tagged regions. The idea is outlined here, or see our AJHG paper for full details.

Originally, all these tools required individual-level data (genotypes and phenotypes). We have recently added SumHer, which allows you to do lots of cool things using just summary statistics.

LDAK also includes MultiBLUP, our method for creating linear prediction models. This improves upon standard BLUP by allowing for multiple kinship matrices (see our Genome Research paper here). Either the user can provide these kinship matrices, or they can be determined using Adaptive MultiBLUP.
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Please email doug<dot>speed<at>ucl<dot>ac<dot>uk with any questions or bug reports.