mobster

NGS tool for detecting MEI and gene retrotransposition events in WGS and WES data, see Thung et al. Genome Biol. 2014 for more information.

Install

Dependencies

• Mobster depends on an aligner for aligning potential reads to mobiome reference. By default MOSAIK is the aligner of choice, which can be installed via bioconda or cloning the MOSAIK git repository.

• Mobster is written in Java (tested working with Java 8), and built using maven, hence assumes that they are in your PATH.

• git lfs is required. See this link for more detail.

Simple installation

To build mobster simply run "install.sh". This will package the required classes into a fat executable jar in the "target" directory. Typically called MobileInsertions-<version>.jar. For example MobileInsertions-0.2.4.1.jar.

After installation, the aligner of choice (e.g. MOSAIK) is assumed to be in the PATH. If not, please don't forget to update Mobster.properties to include the location for the aligner.

Testing the installation

Try running Mobster with the sample bam provided

cd target
java -Xmx8G -jar MobileInsertions-0.2.4.1.jar \
    -properties Mobster.properties \
    -out TestSample

Example on how to call the program for a single sample:

java -Xmx8G -jar MobileInsertions-1.0-SNAPSHOT.jar \
    -properties Mobster_latest.properties \
    -in input.bam \
    -sn test_sample \
    -out mobster_test

You can also run the program in multiple sample mode. For this you need to change MULTIPLE_SAMPLE_CALLING in the properties file to true. Then you can run Mobster like:

java -Xmx8G -jar MobileInsertions-1.0-SNAPSHOT.jar \
    -properties Mobster_latest.properties \
    -in A1_child.bam,A1_father.bam,A1_mother.bam \
    -sn A1_child,A1_father,A1_mother \
    -out A1_trio_mobster

Important:

• Due to their size the test files and a number of resources for Mobster are stored with git lfs. These will not be retrieved with the initial git clone, but will be downloaded when you run "install.sh".
• If you want to turn on multiple sample calling, make sure you set the property MULTIPLE_SAMPLE_CALLING to "true" (the default is "false").
• You can set the READ_LENGTH property to the appropriate value for your BAM file in the properties file.
• In this version of Mobster, Mobster will accept BAM files produced by different mappers. In the property file MAPPING_TOOL is set to "unspecified" and MINIMUM_MAPQ_ANCHOR is set to 20. I would leave this as is.
• Most of the other default settings in the property file should be fine, to be a bit more sensitive you can lower the MINIMUM_POLYA_LENGTH to 7.