Overview

Set random bases in a read to 'N' according to a downsampling probability and its quality to 0. In this task all reads are considered, even those that do not pass the usual SAM flag filters.

Input

• A BAM file

Output

• A BAM file

Usage example

./atlas task=downsampleReads bam=example.bam fraction=0.1 verbose #every 10th base will be set to 'N'

Specific arguments

• fraction : The probability with which a base will be set to 'N'

Engine Parameters

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