These six options can be added to most commands:
--extract <extractfile> - tells LDAK to use only the predictors specified in <extractfile>.
--exclude <excludefile> - tells LDAK to not use the predictors specified in <excludefile>. Note that predictors in --exclude <excludefile> takes priority over predictors in --extract <extractfile>.
--chr <integer> - tells LDAK to only use predictors on a particular chromosome. If you use --chr AUTO, LDAK will only use Chromosomes 1-22 (in humans, these are the autosomes).
--snp <predname> - tells LDAK to only use the named predictor.
--keep <keepfile> - tells LDAK to only use the samples specified in <keepfile>.
--remove <removefile> - tells LDAK to not use the samples specified in <removefile>. Note that predictors in --remove <removefile> takes priority over predictors in --keep <keepfile>.
In addition, for many commands, you can add --pheno <phenofile> and LDAK will only consider samples for which phenotypes are available.
Note that if you would like to filter predictors based on minor allele frequency, variance, missingness or information score, you must first remake the data (this filtering can not be done on-the-fly).
