Mach-admix: fatal error with physical map?

Question

[Laura]

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?

[kristincilla_16]

Did you get solve this problem?

I have the same problem, I have check the .ped and all my markers are in the same chr, all positions are unique an they are all ordered by physical position

I don't what I can do...

Answer 1

[Laura]

Hi, I had this problem when using mach-admix for Windows. Once I tried using it for Linux, it did not happen again.