Overview

This task creates a table summarizing the composition of the bases covering each site. It is basically a flattened 4-dimensional table.

Input

• A BAM file

Output

A table with the following columns. Each line represents a possible allelic composition.

• A,C,G,T: 4 columns listing the amount of bases of each type.
• Counts: the number of sites that have this specific base composition
• Depth: the total depth of the base composition (equal to sum of columns A,C,G and T)

Usage example

./atlas task=allelicDepth bam=example.bam maxAllelicDepth=5

Specific Arguments

• maxAllelicDepth: All sites with a base type that has higher depth will be ignored. Set this to at least the average depth across sites.

Engine Parameters

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