Overview

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.

Input

• A BAM file

Output

• A table called example_depthPerWindow.txt with the window coordinates and their mean coverages

Usage Example

./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

Engine parameters that are common to all tasks can be found here.