This page describes some advanced settings.
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All features allow you to add the option –workdir <directory> to specify the working directory. LDAK will then prefix any relative filenames with <directory>. This option is useful when running on a cluster that requires absolute filenames (and does not allow the option -cwd). For example, if Calculating Statistics using the command
./ldak.out –calc-stats output –bfile data –work-dir /home
LDAK will look for the data files /home/data.bed, /home/data.bim and /home/data.fam, and will write results to /home/output.stats and /home/output.missing.
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All features allow you to add the option --random-seed <integer> to specify the seed used for random number generators. Note that this option only has an impact for stochastic features, for example when using the command --calc-genes-reml <folder> as part of a Gene-Based Analysis or when using LDAK-GBAT.
For example, if you run the commands
./ldak.out --cut-genes genes --bfile human --genefile anns.txt
./ldak.out --calc-genes-reml genes --pheno quant.pheno --bfile human --ignore-weights YES --power -.25
./ldak.out --join-genes-reml genes
two times, then the results of each run will be slightly different (specifically, each run will use different permutations, so the permuted p-values will change slightly). However, if you instead run the commands
./ldak.out --cut-genes genes --bfile human --genefile anns.txt
./ldak.out --calc-genes-reml genes --pheno quant.pheno --bfile human --ignore-weights YES --power -.25 --random-seed 7
./ldak.out --join-genes-reml genes
two times, the results of each run will be identical.
