Loading PLINK files to Haploview
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3.7 years ago
rmf ★ 1.3k

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 • 4.1k views
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2
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3.7 years ago

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

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2.1 years ago
Shicheng Guo ★ 8.8k

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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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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