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Loading PLINK files to Haploview

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.

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

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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?

plink haploview snp
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updated by Nai • Nai • written by firestar firestar

2 answers

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

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written by mbyvcm mbyvcm

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

plink --file <input_prefix> --recode HV --snps-only just-acgt --out <output_prefix>
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written by Shicheng Guo Shicheng Guo

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

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written by Nai • Nai

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