Download. Jump to Page. You are on page 1of Search inside document. Haploview Documentation. Haploview Documentation 25 Updates. General Linux Documentation: Haploview requires a large amount of memory so it is recommended that you request more memory through the isub command. You can still use Haploview to analyze your own data as long as you have a PED file and an INFO file as explained in Haploview documentation. Therefore.
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Does someone already have this code written? I need to make slight correction to the above: Hi Silven, I am not familiar with Haploview. One would think that it would be able to extract the information necessary and ignore the extra samples. Are you able to copy the error message you have?
VCF to PED Converter
As far as I can tell from trial-and-error, the refers to a specific sample that has wrong data, whatever may be wrong. Probably focumentation many bases at a SNP site: Here are exact quotes of two error messages: The Haploview documentation at https: Please note that Haploview can only interpret biallelic markers with greater than two alleles e.
You need to remove the problematic snps. This can be done by Plink version 1.
Please not that Plink 1. You can download it here: With that said, you will need to use the command line in order to run your file cleanup. haplovieww
To remove certain individuals from a file: One must combine this option with the desired analytic e. Since you are not familiar with the command line, let me guide you a bit more thoroughly: I will work with that code and post here if I get stuck.
Pupasuite – Haplotype documentation – Bioinformatic Department Projects
Next week I will actually try manipulating files. We found a fix using UNIX commands only, like the sample below. Probably a project over the holiday break. The PED file first 6 columns have non-marker info, so column numbers are adjusted by 6. We got files that fixed that problem marker, and then HaploView gave us a new problem marker.
Whole genome association analysis toolset
And just let us know if you need any help in the future. Silven asked 1 year ago. Silven replied 1 year ago. Eloi Mercier Staff answered 1 year ago. Eloi Mercier Staff replied 1 year documentatiln.