I'm trying to impute using Mach-Admix. The ref file is 1000G P3,v5, downloaded from MACH website. I'm imputing using chromossome chunks of 5Mb and flanks of 250kb).
In my sample file there are ~800 markers (from the same splitted chromosome region) and 900 individuals.
The program shows this message:
Physical map will be used to improve crossover rate estimates.
FATAL ERROR -- Problems with physical map ... Before continuing, check the following: * All markers are on the same chromosome * All marker positions are unique * Markers in pedigree and haplotype files are ordered by physical position
1. The physical map is only an optional file. So I did not used it in the command line.
2. Even when impute along with the physical map I get the same message (map in the format "chr marker_name position"). All my markers are in the same chr (4).All positions are unique. They are all ordered by physical position.
Has anyone had this problem?