Loading PLINK files to Haploview

Question

[firestar]

I can't seem to get Haploview to accept PLINK files. I downloaded the 'sample.ped' and 'sample.info' trial files from this haploview website.

I am loading the .ped file for 'Results File:' and the .info file for 'Map File:'. All other options are left at default.

And I get the error: 'Improper map file formatting on line 1'

My Haploview version is 4.2 (16-Feb-2010).

I also get the same error with my own data why is why I tried the sample data from the Haploview website. Anyone has any suggestions?

Answer 1

[christopher medway]

Open as "Linkage Format" - .ped file goes into the 'Data File' field; .info into 'Locus Information File.'

Answer 2

[Shicheng Guo]

convert plink file to haploview input with plink v1.09:

plink --file <input_prefix> --recode HV --snps-only just-acgt --out <output_prefix>

[Nai]

Haploview is showing 0% loading by inputting the file "plink --file <input_prefix> --recode HV --snps-only just-acgt --out <output_prefix>" in linkage format