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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Synthesis-View is a data visualization application. Through the use of stacked data-tracks, information on SNP genomic locations, presence of the SNP in a specific study or analysis, as well as related information such as genetic effect size and summary phenotype information, are available for plotting according to user preference.

This file is required and contains information for plotting the p values and effect size beta values for the SNPs in the results.



The file must be a text, tab-delimited file with a header line. The ha;loview of columns does not matter in this file but the column names do.

There are 3 required columns: If absent, the SNP column is used. The colors can be specified in one of several formats that RMagick understands.

Cleaning UCSC PED files for Haploview • Canadian Bioinformatics Helpdesk

SNPs that do not have position information the Synthesis-View standard file are excluded from the plot. Columns need to have a valid docmuentation specified.

Valid types are pval p valuees effect sizebetauci effect size upper confidence intervalbetalci effect size lower confidence intervalN sample sizecaf coded allele frequencydocumdntation total casescontrols total controlscafcases coded allele frequency for casescafcontrols coded allele frequency for controlspower and study number documentatio studies included. Alternatively, to create a forest plot view, the file may contain columns for odds ratio results and upper and lower confidence intervals.

These results than can then be plotted in conjunction with the ‘Produce forest plot?


Cleaning UCSC PED files for Haploview

To specify colors for the groups use the column header Color. Group documwntation and phenotype averages can be shown using the following columns: Samples sample-size for each groupAvg Pheno the mean of the phenotype for that respective groupand Std Dev standard deviation of the respective phenotype.

Columns that create a box plot of the summary information are: This optional file lists information for genes represented in the results.

It typically gives position information for genes. The first line contains header columns as below.

This tab-delimited file lists expanded definitions for the identifiers in the Synthesis-View Standard File.