writeDepthPerWindow calculates the mean sequencing depth for non-overlapping sliding windows in a BAM file. The mean depth per window is calculated as the aligned bases in the window divided by the window length.
- A BAM file
- A table called example_depthPerWindow.txt with the window coordinates and their mean coverages
./atlas task=depthPerWindow bam=example.bam verbose
You can calculate the sequencing depth for custom windows:
./atlas task=depthPerWindow bam=example.bam window=custom_regions.bed verbose
Engine parameters that are common to all tasks can be found here.