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Reads based Genotyping Tools Setup

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Olivo Miotto edited this page May 18, 2021 · 1 revision

Building the tools

Clone the GeneticReportCard repository. This contains two projects:

  • AnalysisCommon contains library that are shared by multiple projects (and which will probably be packaged separately eventually).
  • SequencingReadsAnalysis contains the sources for the reads analysis tools (grc and sample classification)

Ensure that Java JRE 1.8 or higher is installed; test using

java –version

Set working directory to the root folder of SequencingReadsAnalysis project and type

ant build

The Ant task should build both projects.

Running the tools

Running the tools requires Java JRE 1.8 or higher (see above). The tools use several third-party libraries, which are stored in the /lib folders of each project. These must be added to the Java class path, as must the /bin folders of both projects. The following is a set of commands that sets the classpath:

GRCC =/path/to/clone/of/GeneticReportCard/AnalysisCommon
GRCA =/path/to/clone/of/GeneticReportCard/SequencingReadsAnalysis
CLASSPATH=$GRCA/bin:$GRCC/bin:\
$GRCC/lib/commons-logging-1.1.1.jar:\
$GRCA/lib/apache-ant-1.8.2-bzip2.jar:\
$GRCA/lib/commons-compress-1.4.1.jar:\
$GRCA/lib/commons-jexl-2.1.1.jar:\
$GRCA/lib/htsjdk-2.1.0.jar:\
$GRCA/lib/ngs-java-1.2.2.jar:\
$GRCA/lib/snappy-java-1.0.3-rc3.jar:\
$GRCA/lib/xz-1.5.jar

You need to ensure that the Java tools can allocate sufficient memory. Unfortunately I have not been able to do rigorous testing, and memory usage seems to be largely determined by the Broad BAM processing libraries. An allocation of 2GB seems to work; set this with

java -Xms512m -Xmx2000m <class> <params...>

Running the tools

The GRC tools and Sample Classification tools are run separately. Please refer to the documentation at their respective pages:

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