qMule

• Introduction
• Installation
• Modes

Introduction

qmule is a collection of small but useful routines for operating on files associated with next-generation sequencing. It is a stand-alone java app that is a intentionally structured after the samtools model of a single executable where the first commandline parameter picks which mode to execute, and each mode has it's own collection of commandline options. The mule modes are each described on separate wiki pages linked from the table below.

Installation

qmule requires java 7 and has different compute and memory requirements deepening on the mode.

To install qmule:

• Download the qmule tar file
• Untar the tar file into a directory of your choice

You should see jar files for qmule and its dependencies:

[oholmes@minion0 qmule]$ tar xjvf qmule.tar.bz2
jopt-simple-3.2.jar
picard-1.110.jar
qcommon-0.1pre.jar
qio-0.1pre.jar
qmule-0.1pre.jar
qpicard-0.1pre.jar
sam-1.110.jar
[oholmes@minion0 qmule]$

qmule modes are invoked by directly naming the class that is to be executed as can be seen in the example below:

usage: qmule org.qcmg.qmule.AlignerCompare -i <bam1> -i <bam2> -o <output prefix with full path>

Modes

Mode	Description
AlignerCompare	Compare 2 BAMs aligned from the same FASTQ and separate out reads that are different between the BAMs
BamMismatchCounts	For reads that mapped full-length, provide a tally of how many mismatches were in each read
MafFilter	Search for QCMG-annotated MAF files within a specified directory and apply QCMG-specific filters to produce 2 MAF files - high and low confidence