qprofiler
is a standalone Java app that takes in BAM or FASTQ files and provides an XML file containing basic summary statistics for each file. If no output file is specified (a supplied file with a .xml
extension is considered an output file), then the process will write to a default file (currently qprofiler.xml
).
While the XML file is useful for extracting values for further analysis, a visual representation of the data is more useful in most cases so another tool (qvisualise) was created to parse the qprofiler XML files and produce HTML output with embedded graphs.
qProfiler uses the Picard library to access BAM files.
You should see something like this:
[oholmes@minion0 test_adama_tools_data]$ tar xjvf qprofiler.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 qprofiler-1.0.jar qvisualise-0.1pre.jar sam-1.110.jar [oholmes@minion0 test_adama_tools_data]$
java -jar qprofiler-1.0.jar -input <full_path_to_input_bam> -output <full_path_to_output_xml> -log <full_path_to_log_file> -ntC <number_of_consuming_threads> OPTIONAL -ntP <number_of_producing_threads> OPTIONAL -validation Possible values: {STRICT, LENIENT, SILENT}
For example, to run on a 16 core node:
java -jar qprofiler-1.0.jar \ -input /sample_virus.BWA-backtrack.bam \ -log /sample_virus.BWA-backtrack.bam.qp.log \ -output /sample_virus.BWA-backtrack.bam.qp.xml \ -ntP 4 -ntC 16
NOTE that BWA mapped bam files may need to be run with the optional parameter -validation SILENT
otherwise Picard will throw an exception.