Help with --make-bed from --pfile

[Elielson Veloso]

Hello! I  am working with a Plink2 pfile dataset and would like to run an Haploview analysis. Since --recode HV is not currently available directly from pfile, I tried to use --make-bed to generate Plink 1.9 readeble files back so that I can use --recode HV properly. When running --make-bed I added the --keep-allele-order flag so that REF and ALT alleles would not be swiped from pfile to binary files, however, it did not work and REF and ALT alleles order changed in my generated .bim file. I would like to know if there is any other way to prevent REF/ALT allele swipe in this case... if not, would plink 2 give me any option to run an haplotype analysis without the need of using Haploview??

Thanks in advance,

Elielson'

[Christopher Chang]

https://www.cog-genomics.org/plink/2.0/formats#bim

Note the *intended* order.

[Elielson Veloso]

Thanks again! I mean, what would be the right way ( and steps) to start from a pfile, going to a bfile and then generating haploview (.ped, .info)?  

I would be really greatful if you could guide me on that!!

Thanks in advance