AdamaJava Wiki
Status: Alpha
Brought to you by:
grendeloz
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.
qmule requires java 7 and has different compute and memory requirements deepening on the mode.
To install qmule:
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>
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 |