Filtering in a SNP-Tree creation scenario
To construct a SNP tree, all sample data must have been analyzed (i.e., reads mapped and variants called) using the same reference sequence. If we want to use all the samples that were generated by the Map to Specified Reference workflow on several occasions using a common reference sequence, we use the quick filtering options.
- Filter all samples where read mapping and variant calling was performed using a common reference by clicking on the icon () and using the following filter parameters: in the first drop-down menu, choose the column whose header is the reference sequence of interest; in the second drop-down menu, choose the term "contains"; and in the third window, write "true".
- Select all remaining samples.
- Click on the Find Associated Data () button. This opens the Metadata elements table underneath the initial Metadata table with a certain amount of elements associated with the samples selected in the Metadata Result Table.
- Click on the Quick Filters () button in the Metadata Elements Table (bottom view) and select the Filter Re-mapped 'common reference' for SNP Tree option.
- Select all the remaining elements.
- Click on the With selected () button and select the Create SNP Tree option. The Create SNP Tree wizard (described in Create SNP Tree) is displayed. The read mappings are preselected as input. The variant tracks and the Result Metadata Table are automatically preselected as parameters.