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:
./ldak.out --cut-genes genes --bfile data --ignore-weights YES --chunks-bp 75000
and here is the screen output:
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
LDAK - Software for obtaining Linkage Disequilibrium Adjusted Kinships and Loads More
Version 5.2 - Help pages at http://www.ldak.org
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
There are 4 pairs of arguments:
--cut-genes genes
--bfile data
--ignore-weights YES
--chunks-bp 75000
Error reading data.bed; check file exists and is not empty
