Help

If you have any questions about LDAK, or spot any errors in the program or in the instructions, please email me: doug <dot> speed <at> ucl <dot> ac <dot> uk

When asking questions about LDAK, please SEND both the COMMANDS you ran and the SCREEN OUTPUT for each - 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.out --cut-genes genes --bfile data --ignore-weights YES --chunks-bps 75000

and here is the output:

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LDAK - Software for obtaining Linkage Disequilibrium Adjusted Kinships and Loads More
Version 5.0 - 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

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

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Reading IDs for 5200 samples from data.fam

Reading annotations for 39892 predictors from data.bim

Data contain 5200 samples and 39892 predictors

5703 chunks were found, spanning 39892 unique predictors and divided into 1 partition.
The details are saved in genes/genes.details and genes/genes.predictors.used
The longest chunk contains 105 predictors

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Mission completed. All your basepair are belong to us 🙂
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