Overview

Create a BAM file with binned quality scores according to the bins defined by illumina .

Specifically, quality scores will be binned as follows:

In this task all reads are used, even those that do not pass the usual SAM flag filters.

Input

• A BAM file

Output

• A BAM file

Usage Example

./atlas task=binQualityScores bam=example.bam

Engine Parameters

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