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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Haploview’s Tagger operates in either pairwise or aggressive mode. Silven replied 1 year ago. Tagger avoids overfitting by only constructing multi-marker tests from SNPs which are in strong LD with each other, as measured by a pairwise LOD score.
We found a fix using UNIX commands only, like the sample below. After this, it tries to “peel back” the tag list by replacing certain tags with multi-marker tests.
Follow us Blog Twitter Facebook. The program Haploview Barrett et al. Can be specified more than once for multiple populations.
VCF to PED Converter
A block can be considered a region with a low recombination rate and consequently can be properly described with a unique SNP. This file is required and contains information for plotting the p values and effect size beta values for the SNPs in the results.
Since you are not familiar with the command line, let me guide you a bit more thoroughly: Columns need to have a valid type specified. If the input file is only remotely accessible then it must be compressed by bgzip and indexed by tabix. It typically gives position information for genes. I need to make slight correction to the above: There are a number of differences between the implementations, although they are constructed around the same concept.
I will work with that code and post here if I get stuck. The order of columns does not matter in this file but the column names do.
Whole genome association analysis toolset
Hi Silven, I am not familiar with Haploview. If the vcf file is compressed then you must have tabix installed. The PED file first 6 columns have non-marker info, so column numbers are adjusted by 6. Alternatively, to create a forest plot view, the file may contain columns for odds ratio results and upper and lower confidence intervals.
Certain markers can be forced into the tag list or explicity prohibited from being chosen as tags. Haplovieew file must be a text, tab-delimited file with a header line.
Cleaning UCSC PED files for Haploview
Probably too many bases at a SNP site: Synthesis-View is a data visualization application. To specify colors for the groups use haplovifw column header Color. Aggressive tagging introduces two additional steps. The parameters of those algorithms are the default ones as described in the Haploview documentation.
Pupasuite – Haplotype documentation – Bioinformatic Department Projects
Other two methods are used: As far as I can tell from trial-and-error, the refers to a specific sample that has wrong data, whatever may be wrong. Group totals and phenotype averages can be shown using the following columns: These results than can then be plotted in conjunction with the ‘Produce forest plot?
This optional file lists information for genes represented in the results. One must combine this option with the desired analytic e. Samples sample-size for each groupAvg Pheno the mean of the phenotype for that respective groupand Std Dev standard deviation of the respective phenotype.