Help

If you have a problem when running LDAK, please make sure you are using the most current release (obtain the latest version from Downloads, then try the command again).

If you are having problems with the example commands, please be aware that you should replace ./ldak.out with the name of the LDAK executable you obtained from Downloads (e.g., replace ./ldak.out with ./ldak5.1.linux or ./ldak5.1.mac).

If you have still have a problem, or find any errors in the software or the instructions, you are very welcome to email me: doug<at>qgg<dot>au<dot>dk

When asking questions about LDAK, please SEND both the COMMANDS you ran and the SCREEN OUTPUT these produced (this makes understanding your questions much easier).

For example, this is a bad question:

Hi Doug, I'm having trouble with --cut-genes

Whereas this is a good question:

Hi Doug, I'm having trouble with --cut-genes. This is the command I used:

./ldak5.1.linux --cut-genes genes --bfile data --ignore-weights YES --chunks-bp 75000

and here is the screen output:

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LDAK - Software for obtaining Linkage Disequilibrium Adjusted Kinships and Loads More
Version 5.1 - Help pages at http://www.ldak.org
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There are 4 pairs of arguments:
--cut-genes genes
--bfile data
--ignore-weights YES
--chunks-bp 75000

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Cutting predictors into overlapping chunks of length 75000 basepairs (to avoid overlap, add "--overlap NO")

If you plan to use "--calc-genes-kins" or "--calc-genes-reml", consider adding "--partition-length" or "--by-chr YES" to divide chunks into partitions (which will allow the next step to be parallelized)

If you add "--pvalues", LDAK will work out the lowest p-value for each chunk

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Reading IDs for 5200 samples from data.fam

Reading details for 39892 predictors from data.bim

Data contain 5200 samples and 39892 predictors

5705 chunks were found, spanning 39892 unique predictors and divided into 1 partition; the longest chunk contains 105 predictors

Details saved in genes/genes.details and genes/genes.predictors.used

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Mission completed. All your basepair are belong to us 🙂
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