problem of "ordering in physical positions" phasing SNPs with Shapeit
The manual suggests that each &quot;chromosome&quot; needs to have its own input file.

You have to split the dataset by chromosomes. ShapeIT can just phase one chromosome at a time. If you are working on GWA data, you can proceed as follows:

for chr in $(seq 1 22) ; do plink --file example --chr $chr --recode --out example_chr$chr ; done

You will obtain 44 files; example_chr1.ped, example_chr1.map, ..., example_chr22.ped, example_chr22.map that you can phase separately.