What to do if your input files were not created with PLINK?
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It is preferrable to work with PLINK output files to avoid
making mistakes with preparing the RelOut input files. 
However, if you prepare your files in another way, 
please follow these instructions:


1. Add "-plink-style no" to your command line.

Example: ./RELOUT32 -gfile relatives.genome -lowlim 0.1 -plink-style no -out remove_these_individuals.txt

This is opposed to the "-plink-style yes" which is the default
bahavior of RelOut.


2. The genome file (gfile) must have the following format:

a) no header
b) tab-delimited
c) The file must have 5 columns: FID1	IID1	FID2	IID2	DISTANCE

FID1 = familiy ID of the first individual (replace with 0, if it doesn't exist)
IID1 = individual ID of the first individual (must be a valid ID)
FID2 = familiy ID of the second individual (replace with 0, if it doesn't exist)
IID2 = individual ID of the second individual (must be a valid ID)
DISTANCE = genetic distance between the first and the second individual

Please note that there must be one row for each genetic distance definition. Each pair
of individuals should be represented only once.


3. The missing/callrate file (mfile) must have the following format:

a) no header
b) tab-delimited
c) The file must have 3 columns: FID	IID	CALLRATE

FID = familiy ID (replace with 0, if it doesn't exist)
IID = individual ID (must be a valid ID)
CALLRATE = call rate value 

Note that PLINK's missing file (mfile) contains "missing values" 
instead of "call rate values" but here the CALLRATE column
must contain the call rate values (1-missing). RelOut will treat 
the values correctly when this requirement is followed.


4. The phenotype file (pfile):

This file is prepared the same way whether or not PLINK was involved.


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QUESTIONS?

E-mail: RelOut <at> ToomasHaller.com