I'm trying to phase my data (whole genome resequencing SNPs) with Shapeit (from ped file) and I get this error message :
[33mERROR:[0m Wrong ordering in physical positions curr_pos=54 prev_pos=65
I found that it's due to the fact that my .map file is like this (4 columns):
Chromosome_number SNP_ID SNP_genetic_position SNP_physical_position Contig100131 . 0 65 Contig100220 . 0 54
And Shapeit only looks at
SNP_physical_position but does not check if the SNPs are on the same contig or not and so it says it is not happy because position 54 is after 65!
How could I make it understand that the positions are not in the same contig and so there is no mistake? Must I run Shapeit per contig (I have a lot of them so I hope not)?