Target Region Coverage Analysis

The Target Region Coverage Analysis tool makes it easy to evaluate and compare multiple samples with respect to a given coverage metric. The tool takes as input one or more per-region statistics tracks generated by QC for Targeted Sequencing and outputs a target region track providing statistics across the analyzed samples. In addition, an overlay annotation track (for example a gene track) can be provided to obtain a higher-level summary, where target regions are grouped based on overlap, and coverage statistics are calculated for each group.

The QC for Targeted Sequencing tool is described in QC for Targeted Sequencing

Running the tool

To launch Target Region Coverage Analysis, go to:

        Toolbox | Quality Control (Image quality_control_closed_16_h_p) | Target Region Coverage Analysis (Image target_region_coverage_16_h_p)

In the first dialog (figure 29.14), select one or more per-region statistic tracks (Image annotation_track_16_n_p) produced by QC for Targeted Sequencing. The tracks must be based on the same target region track.

Image targetregioncoverageanalysisstep1
Figure 29.14: Select one or more per-region statistics tracks.

The next dialog allows you to configure the settings for this tool, as shown in figure 29.15 and described below.

Image targetregioncoverageanalysisstep2
Figure 29.15: Settings of the Target Region Coverage Analysis tool.