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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

Please see the Java documentation for additional information on running java processes in jobs.

References