Visualize aneuploidy analysis results
You must have IRGV set as the default viewer for this procedure. For more information, see Set IRGV or IGV as the default viewer.
- Under the Analyses tab, click Overview.
Select one or more analyses then click Visualize.
The Analysis Visualization screen opens to the IRGV tab. A copy number histogram for each analysis selected appears, with ploidy maps for selected chromosomes or chromosome regions, and karyograms that show copy number gains and losses.
Above the whole genome view for each analysis is a metric known as Productive Reads. It is the sum of mapped reads from a sample that align to the autosomes and chrX in females or to the autosomes and chrX + chrY in males. If the Remove Duplicates CNV finding parameter is set to True, then the Productive reads metric excludes duplicates. Productive reads are the specific reads that are used to establish the relative coverage of tiles across the sample.
Note: If you select multiple analyses generated from analysis workflows with different filter chains with different confidence settings, the software will use the filter chain with the lowest confidence setting and apply that filter chain across the group. You can adjust the Filter Chain and Mapd filters with the controls in the lower right corner of the screen.