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ATLAS / Auxiliary Tools: binQualityScores

Overview

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

Specifically, quality scores will be binned as follows:

Original quality score Binned quality score
2–9 6
10–19 15
20–24 22
25–29 27
30–34 33
35–39 37
≥ 40 40

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.

Updated