Wrong ordering in physical positions

[zillurbmb51]

Hi,
I was trying to phase my genotype data using shapeit2 after qc with plink. Shapeit2 is giving me error:
Wrong ordering in physical positions curr_pos=#### prev_pos=####
Is there any way to fix this issue?
I have tried to use --update-chr and --update-map with HRC reference panel but the error exist.
Any help?

[Christopher Chang]

It sounds like you need to use --sort-vars on your dataset.

[zillurbmb51]

Thanks a lot. I was trying to use as : plink2 --bfile my_plink --sort-vars --make-bed --out my_plink_sorted
It produces bim and fam file but not bed. The message is: Error: Fixed-width .bed/.pgen output doesn't support sorting yet. Generate a regular sorted .pgen first, and then reformat it.

Any help? How could I create a regular sorted bed file?
chr1.step12.log

[zillurbmb51]

Then I tried to make pgen first and then bed but failed. If I use plink2 --bfile chr4.step11 --sort-vars n --make-pgen --out chr4.step12
and then plink2 --pfile chr4.step12 --make-bed --out chr4.step13

and try phasing chr4.step13 but it gives me previous error: Wrong ordering in physical positions curr_pos=77809318 prev_pos=190915650

[Christopher Chang]

Please post usage questions like this in the plink2-users Google group, not here; and make sure to include full .log files.