The original purpose of LDAK was to create kinship matrices adjusted for linkage disequilibrium. The main two steps are:
1 – calculate weightings which reflect the local patterns of correlations across predictors.
2 – (given these weightings) calculate pairwise kinship estimates across samples.
When calculating weightings using population GWAS data, we advise keeping the LD decay parameters at their default values, but you may wish to change these when considering highly structured or related datasets (e.g. those used in plant or animals breeding).
Sometimes it is advisable to use the Subset Options when calculating weightings, particularly when considering a case-control study. LDAK also provides options to facilitate Genomic Partitioning, and arguments for adding and subtracting kinship matrices or converting kinships stored in alternative formats.
Method Overview provides details on the nitty gritty of how LDAK adjusts for LD.
If you have any problems, get in touch: doug<dot>speed<at>ucl<dot>ac<dot>uk.