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ATLAS / Sequence Data Processing Tools: downsample


This task creates downsampled BAM files that contain a specified percentage of the original number of reads. More than one percentage / probability can be specified, and thus allows the creation of several downsampled BAM files at a time. In this task all reads are considered, even those that do not pass the usual SAM flag filters.


  • BAM file


  • Downsampled BAM file(s) with suffix "_downsampled*Prob*.bam"

Usage Example

Create three downsampled BAM files, with 75%, 50% and 25% of the reads respectively:

./atlas task=downsample bam=example.bam prob=0.75,0.5,0.25

Create six downsampled BAM files, with three replicates of the 75% files:

./atlas task=downsample bam=example.bam prob=0.75{3},0.5,0.25

Specific Arguments

  • prob : vector of percentages of reads to be kept in the downsampled BAM files. It is possible to obtain replicates by adding the desired number of replicates in curly brackets {} after the concerned percentage.

Engine Parameters

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