This app uses the calculated Sambamba coverage bed files for x samples to visualise the variability in coverage at each genomic region across all these samples. Results are available as an interactive plot, simplified pdf plot, and csv table.
This app can be used during the development of new diagnositic tests to identify regions which have low coverage.
This app requires the following inputs:
- Name of project containing the samabamba output folder coverage/raw_output/.
At the core of the app is a dockerised R script which reads in all data from the folder coverage/raw_output/ in the project, cleans up the data, and outputs html, pdf, and csv reports.
This app outputs:
- An inteactive HTML report with boxplots of every region sorted by coverage from low > high
- A static plot showing the average for each region
- A csv file with the region data in tabular form
- The app currently does not work with files created with MokaCan - the presence of any of these output files in the input folder will cause the script to stall as it tries to plot > 100,000 data points.
- Currently outputs are not defined in the dxapp.json causing an error message when the app completes - the output folder is instead uploaded via a hardcoded line in the shell script and placed in coverage/uniformity_metrics/ within the named project.
- Currently you cannot define input files - the script looks in a predefined folder for the input and this filepath is hard-coded into the script.