depthPerSiteDist produces the distribution of the sequencing depths per site.
- A BAM file
- 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
./atlas task=depthPerSiteDist bam=example.bam maxDepth=50 verbose
- 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 that are common to all tasks can be found here.