All of the Tagger thresholds can be reset to theirdefault values using the "Reset Thresholds" button. A minimum design score threshold can alsobe specified. Design score files should contain two columns containing the SNP and the design score to assign to that SNP. Design scores can also be loaded in using the "Design Scores" button. The "Alleles to Capture" button also takes in a file with a single column of SNPs to be captured. These buttons take in a file with a single column of SNPs to include or exclude. You can load a set of SNPs to include or exclude using the "Load Includes" and "LoadExcludes" buttons. Additionally, you canspecify the maximum number of tags to pick, as well as the minumum distance (in base pairs) between picked tags. Beneath these buttons are several additional tagging options.You can choose from among pairwise and two aggressive tagging strategies discussed above.You can also set the r 2and LOD thresholds as previously mentioned. Use "Include All"to check all of the "Force Include" boxes, and "Exclude All" to check all of the "Force Exclude" boxes."Uncapture All" will uncheck the "Capture this Allele?" column for all markers, "Exclude A/T and C/G SNPs"will exclude check the "Force Exclude" boxes for SNPs with strand issues, and "Reset Table"will return the table to its initial state. The include and exclude checkboxes are mutually exclusive, and"Capture this Allele" must be checked in order to either include or exclude a marker.ĭirectly below the marker list are buttons to quickly manipulate the table above. If this box is checked, Haploview will include this SNP in the list of alleles to be captured by the chosen tag set. There are three checkboxes for each SNP:Ĭhecking this box will force this SNP to be chosen as a tag SNP.Ĭhecking this box will prohibit this SNP from being chosen as a tag SNP. SNPs which are deselected in the Check Markers tab will not be in this list. This panel shows all SNPs available for tag selection. N.B.Haploview's Tagger requires either an info file or a hapmap style input file, because it references the marker names specified in those files.If you load a pedigree or phased haplotypes input file without an info file, the Tagger panels will not be available. Much more information about the development of this algorithm is available at the Tagger website. This LOD cutoff can be adjusted to loosen or tighten this requirement in general, the default cutoff of 3.0 is appropriate for selecting tags from a HapMap-sized reference panel of 120 chromosomes. 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. After this, it tries to "peel back"the tag list by replacing certain tags with multi-marker tests. these must have been "excluded" since otherwise they would simply be chosen to capture themselves)using multi-marker tests constructed from the set of markers chosen as pairwise tags. The first is to try to capture SNPs which could not be captured inthe pairwise step (N.B. You can also specify which markers in the dataset you want to be captured.Īggressive tagging introduces two additional steps. Certain markers can be forced into the tag list or explicitly prohibited from being chosen as tags. In either case it begins by selecting aminimal set of markers such that all alleles to be captured are correlated at an r 2 greater than a user-editable threshold with a marker in that set. Haploview's Tagger operates in either pairwise or aggressive mode. Tagger currently searches a much broader space of available multi-marker tests (up to 6-mers)whereas Haploview allows only 2- or 3-marker tests in the interest of computational efficiency. It and more information are available at the Tagger website.There are a number of differences between the implementations, although they are constructed around the same concept. Haploview is based on Paul de Bakker's Tagger. Attractive practical features include the ability to force in or exclude sets of tags. We avoid overfitting and unbounded haplotype tests in the association phase by ( a) using only those multiallelic combinations in which the alleles are themselves in strong LD, and ( b) explicitly recording the allelic hypotheses that are to be tested in the subsequent association analysis. We have developed a tagging strategy that combines the simplicity of pairwise methods with the potential efficiency of multimarker approaches. Next Generation in Biomedicine Symposium.Science Writing and Communications Internship.Stanley Center for Psychiatric Research.Genome Regulation, Cellular Circuitry and Epigenomics.Chemical Biology and Therapeutics Science.
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