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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)?

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    $\begingroup$ Why don't you just sort the index file? Will that work? It might still complain if you have multiple instances of the same position, I guess, but try: sed 's/ */\t/g' foo.map | sort -nk4 > new.map and then using the new.map file. If that works, let me know and I will post an answer. $\endgroup$ – terdon Nov 17 '17 at 16:19
  • $\begingroup$ On second thought, that shouldn't work. That would mean you would have the contigs not in order and if the program doesn't take the contig name into account, that would mess everything up. $\endgroup$ – terdon Nov 17 '17 at 18:00
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The manual suggests that each "chromosome" 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.

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  • $\begingroup$ ok, indeed it's written in big in the manual ! When you don't want to see something .... Thanks a lot to both of you for your help ! $\endgroup$ – G. Dumont Nov 20 '17 at 8:15
  • $\begingroup$ @G.Dumont If this answer solved your issue, please take a moment and accept it by clicking on the check mark to the left. That will mark the question as answered and is the way thanks are expressed on the Stack Exchange sites. $\endgroup$ – terdon Nov 20 '17 at 9:50
  • $\begingroup$ what format does the file example need to be in? i.e. what order of columns? header? my map is in order `pos chr cM' $\endgroup$ – Brian Wiley Feb 3 at 22:11

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