qmule
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 qmule modes are each described on separate wiki pages linked
from the table below.
Installation
qmule requires java 21 and has different compute and memory requirements deepening on the mode.
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To do a build of qmule, first clone the adamajava repository. ~~~~{.text} git clone https://github.com/AdamaJava/adamajava ~~~~
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Then move into the adamajava folder: ~~~~{.text} cd adamajava ~~~~
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Run gradle to build qsv and its dependent jar files: ~~~~{.text} ./gradlew :qmule:build ~~~~ This creates the qmule jar file along with dependent jars in the
qmule/build/flatfolder
Usage
java -cp qmule.jar <mode class> [options]
qmule modes are invoked by directly naming the class that is to be
executed as can be seen in the example below:
java -cp qmule.jar org.qcmg.qmule.AlignerCompare -i file1.bam -i file2.bam -o output.txt
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 |
| SubSample | Create a new BAM file with a subsample of reads from an existing BAM file |
| 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 |
| QSamToFASTQ | Convert BAM/SAM file to FASTQ file |