I used plink to generate .bed, .bim and .fam files from .ped and .map files. This conversion worked well.
When I access the .bim file, I find nan in the third column in one of the lines of the .bim file, like this:
1 rs2027305 nan 245672356 A G
This seems to happen after the conversion from .ped and .map file to .bed files. Because of this I am unable to use the .bim file for any analysis and the following error :
ERROR: Problem reading BIM file, line 50602
Kindly let me know if anyone has encountered this and how this should be handled.