![]() ![]() Specify location of the Result metadata table file. If the calculated z-score for a given position is less than the specified minimum value the position is filtered. Defining as the number of most prevalent nucleotide at a position and as the coverage subtracting, the z-score is calculated as If a position is within this distance of a previously used position it will be filtered. Prune distance specifies the minimum number of nucleotides between unfiltered positions.The position is skipped if at least one sample has coverage below this percentage of its own average coverage. Minimum coverage percentage of average required on a given position.The position is skipped if at least one sample has coverage below the specified threshold. Minimum coverage required in each sample on a given position.Include MNVs or not, along with SNVs when building the SNP tree.The variant tracks determine which positions to include in the SNP tree. Select the variant tracks you want to use. The following Parameters may be specified before setting up the algorithm for the construction of the SNP tree (see figure 13.3): 3: Select variant tracks and specify relevant parameters before generation of a SNP tree. Under normal circumstances you would select one variant track for each read mapping given in the input step, but that is not a requirement.įigure 13. The variant tracks need to have the same reference as the previously selected read mappings. Select the variant tracks you want to use (figure 13.3). 2: For selection of all sequence files in a folder, right click and select Add folder contents (recursively). An efficient alternative to these methods is to use the Quick filtering functionality from the Metadata Result Table to filter easily the data and initiate the SNP tree creation.įigure 13. 1: Select read mappings to be included in the SNP tree analysis.Īlternatively, select data recursively by right-clicking on the folder name and selecting Add folder contents (recursively) (figure 13.2), but remember to double check that files relevant for the downstream analysis are selected. Select the relevant read mappings as shown in figure 13.1įigure 13. Microbial Genomics Module ( ) | Typing and Epidemiology (beta) ( ) | Create SNP Tree ( ) ![]() Note that you can only create a SNP tree if you have identified a common reference for the different stains you are trying to type, and used it for read mapping and variant calling for each of these samples. There are two ways to initiate creation of a SNP tree: from the Result Metadata Table (see subsection 9.4) or by running the tool from the Toolbox. The Create SNP Tree tool is inspired by Kaas2014. Download a static license on a non-networked machine.Download a static license on a non-networked computer.Download a license using a license order ID.Licensing requirements for the CLC Microbial Genomics Module.Set Up Amplicon-Based Reference Database.Download Amplicon-Based Reference Database.Download Pathogen Reference Database output report.Visualization of K-mer Tree for identification of common reference. ![]()
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