Loading Data

Loading Data


The first step in analyzing data with Haploview is loading data. When the program starts, a dialog appears which offers several choices in data format. Currently Haploview accepts data as a standard linkage-style file, as a file with partially phased haplotypes, or in dump format from the HapMap Project project. For now, select the default, linkage-style load option shown at right.



Next, you'll be presented with a file selection dialog like the one below. It allows you to choose input files along with some options. If you use the "Browse" button (highlighted in red) to select your linkage file, Haploview will automatically look for a file of the same name with the extension ".info" to use as a marker information file. You can also manually select an info file. Some features (e.g. Tagger, custom association tests) require an info file. Browse now for the sample file sample.ped and make sure Haploview can find the sample info file sample.info

Haploview only computes LD statistics for markers within a certain distance (default = 500Kb). You can adjust this to another value or enter "0" to force computation for all marker pairs. Individuals with more than a certain percentage of missing data are excluded by default. You can adjust this threshold (default = 50%) in the field provided.

Next is an option to do association tests (highlighted in blue). Selecting this checkbox allows you to specify whether your data is family trios or a case/control sample. Select the association checkbox now and leave the "Family trio data" button selected, as the sample dataset is comprised of family trios. It's also possible to provide a file with a list of specific SNPs and haplotypes you'd like tested. More information is available in the documentation; for now just leave the field blank.Click "OK" when you're ready.