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* When PED file has genotypes saved, there is no need for a VCF file as input.
* When PED file has genotypes saved, there is no need for a VCF file as input.
* Rare-Metal-Worker takes PED/DAT file in Merlin format. Please refer to [[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description]] for details.
* Rare-Metal-Worker takes PED/DAT file in Merlin format. Please refer to [[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description]] for details.
* DAT file must have variant names in the following format "M chr:pos". Here is an example of variant name format in DAT file:
* DAT file must have variant names in the following format "M chr:pos". An example DAT file is in the following:
M 1:123456
M 1:123456
M 1:234567
M 1:234567
M X:12345
M X:12345
M X:111111
M X:111111
C SEX
C AGE
C AGE2
T LDL
T HDL
* Orders of labels in DAT file have to match the order of fields in PED file.
* '''Markers in PED and DAT file must be sorted by chromosome and position.'''
* '''Markers in PED and DAT file must be sorted by chromosome and position.'''
