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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.
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