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Qualimap

Qualimap examines sequencing alignment data in SAM/BAM files according to the features of the mapped reads and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data.

Qualimap is available as a module on Apocrita.

Usage

To run the latest installed version of Qualimap, simply load the qualimap module:

$ module load qualimap
$ qualimap -help
usage: qualimap <tool> [options]

For usage documentation, run qualimap -help.

Example job

Summarise a BAM file

Here is an example job running on 2 cores and 4GB total memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G

module load qualimap
qualimap bamqc \
         -bam example.bam \
         --java-mem-size=4G

The main Qualimap utility is a Java program, so please see the Java documentation for additional information on running java processes in jobs.

Qualimap memory use

When submitting a Qualimap job it is important to use the option --java-mem-size as shown in the example above. The program does not consider the memory requested in the job submission script and so without this option the program will allow only the default maximum memory for the Java process. This is currently 1200 MB. The value should be set slightly below the total requested memory to allow most of the job's memory to be used while allowing for some overhead.

References