Overview

This task separates the reads of a BAM file into several new BAM files. Contrary to task downsample, all reads that pass the filters are kept and assigned to different BAM files according to probabilities provided with parameter frac.

Input

• BAM file

Output

• New BAM file(s) with the specified fraction of reads with suffix "_fraction_*.bam"

Usage Example

Create three BAM files, with 75%, 20% and 5% of the reads respectively:

./atlas task=separateReads bam=example.bam frac=0.75,0.2,0.05

Specific Arguments

• frac : vector of percentages of reads to be kept in each created BAM file. The frac percentages are internally normalized to sum to 1.

Engine Parameters

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