How To Generate .Dat File For Imputation In Mach??

Question

[mandar.bobade60]

Hi all

Currently I only have .ped and .map file with me and I want to generate .dat file. Can anybody tell me, how I can generate .dat file for my data, such that I can use it for imputation in MACH.

Thanks in advance,

Mandar R. Bobade

Answer 1

[zx8754]

These links explain it all:

http://www.sph.umich.edu/csg/abecasis/MACH/tour/input_files.html

http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html

Data files can describe a variety of fields, including disease status information, quantitative traits and covariates, and marker genotypes. A simple MACH data file simply lists names for a series of genetic markers. Each marker name appears its own line prefaced by an " M " field code. Here is an example:

<Example of a simple data file>
 M marker1
 M marker2
 ...
<End of simple data file>

Here is an awk to convert .map to .dat:

awk '{print M $2}' mymap.map > mymap.dat

[mandar.bobade60]

Thank you Zx8754.

[Raju]

Hello @zx8754, hereafter converting the .map file to a .dat file and I'm trying to run the below command :

plink --dosage myfile.dat --fam mydata.fam

but throwing an error saying "ERROR: Bad format fdr dosage file, expecting more columns", What does it mean?