Displaying Estimated Haplotype Data: Visual Haplotypes


The visual haplotype function is now available through our Genome Variation Server (GVS). Please update your bookmarks to http://gvs.gs.washington.edu/GVS.

To do so, you will need a .txt file of Phased haplotype data for each individual in the sample population as determined by PHASE. (Such files are available for each of the genes we have resequenced for SeattleSNPs and NIEHS SNPs by clicking the Phased Individual Haplotypes  link on the web page of the gene.) On the GVS home page, click genotype input  in the input from file  field. On the next web page, click the Browse  button, and, in the File Upload  dialogue box, find the .txt file of the Phased haplotype data on your computer; select it and click the Open  button. Then, click the display genotypes  button in the lower left part of the screen. In the resulting pop-up window, click on open graphical display of genotypes  to view the genotype (aka visual haplotype) you have requested.

You can also use GVS to generate a visual genotype. On the GVS home page, you may choose either: 1) to select a candidate gene from our "pga" or "egp" gene lists by clicking the appropriate button in the "seach candidate genes" field; or 2) to upload your own genotype data for processing by clicking "genotype input" in the "input from file" field.

If you choose to select a PGA or EGP candidate gene, you will be taken to the appropriate web page from which you can Select Gene  from a drop-down list. Set the display and analysis parameters as you wish, then, click the display genotypes  button in the lower left part of the screen. In the resulting, pop-up window, click on open graphical display of genotypes  to view the visual genotype you have requested.

If you choose to upload your own genotype data for processing, you will be taken to a web page into which you can upload your data file. Simply click the Browse  button, and, in the File Upload  dialogue box, find the file on your computer, select it and click the Open  button. Set the display and analysis parameters as you wish, Then, click the display genotypes  button in the lower left part of the screen. In the resulting pop-up window, click on open graphical display of genotypes  to view the visual genotype you have requested.
 
 
 
   

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