Overview

depthPerSiteDist produces the distribution of the sequencing depths per site.

Input

• A BAM file

Output

• example_depthPerSite.txt with the cumulative distribution of the sequencing depth per site
• example_normalizedCumulativeDepthPerSite.txt with the normalized cumulative depth distribution
• example_quantilesDepthPerSite.txt with the depth distribution quantiles

Usage Example

./atlas task=depthPerSiteDist bam=example.bam maxDepth=50 verbose

Specific Arguments

• maxDepth: largest sequencing depth that should have its own bin. Counts of sites with higher depth will go into a bin called > maxDepth.

Engine Parameters

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