Hi, I wonder if anyone can help.
I am new to SNP analysis, and am in the process of loading my data into PLINK for analysis, when I received the following message:
ERROR Problem with MAP file line: 8 rs71468368 120639217
So, I am left with not being able to load that data into PLINK.The MAP file line that it tells me is a problem doesn't exist in my MAP file. The SNP it says is the error doesn't exist anywhere in the file, but the location it says that SNP has does exist in my MAP file, but for a different SNP rs6469836.
I wondered if it was to do with the build 37 data that I was using, so I converted everything to build 38 co-ordinates and got the following error:
ERROR Problem with MAP file line: 8 rs71468368 119626977
The same error, but with the co-ordinates updated. Again, this SNP (still!) doesn't exist in my MAP file, but this location refers to the same place as rs6469836 now in build 38 co-ordinates.
If I look up rs6469836 it is where I say it is, but if you look up rs71468368 (that only appears in the error message) then I get the information that it is not mapped to a particular location (and the three options are on different chromosomes to where I am looking).
Any ideas other than just excluding this SNP for now?