mobster

NGS tool for detecting MEI and gene retrotransposition events in WGS and WES data

Publication

Mobster: accurate detection of mobile element insertions in next generation sequencing data.

Thung et al. Genome Biol. 2014

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

The sources can be cloned to any directory:

git clone git@github.com:jyhehir/mobster.git

Then, to build mobster simply run "install.sh".

cd mobster
./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.

For GRCh38 use, the user should unpack the compressed repmask resources:

gunzip alu_l1_herv_sva_other_grch38_accession_ucsc.rpmsk.gz

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.

RepeatMasker file

Mobster needs a GRCh37/GRCh38 repmask library file.

GRCh37/GRCh38

The location of this file is included in the Mobster.properties file:

• GRCh37 (default): REPEATMASK_FILE=../resources/repmask/hg19_alul1svaerv.rpmsk
• The user can change this default value to GRCh38: REPEATMASK_FILE=../resources/repmask/alu_l1_herv_sva_other_grch38_ucsc.rpmsk

WARNING: User should unpack the compressed repmask resources (alu_l1_herv_sva_other_grch38_accession_ucsc.rpmsk.gz) during the install.

Updating the RepeatMasker file (if needed)

You can freely download an updated repmask file from the "http://genome.ucsc.edu/cgi-bin/hgTables". There are many output options, here are the changes that you'll need to make:

• “GRCh37” or “GRCh38” assembly
• "Repeats" group
• "Repeatmasker" track
• “genome” region.
• Select output format as "selected fields from primary and related tables"
• Choose the following output filename: alu_l1_herv_sva_other_grch37_ucsc.rpmsk.tmp or alu_l1_herv_sva_other_grch38_ucsc.rpmsk.tmp.
• Cick the "get output" button
• Select all fields (click the "check all" button)
• Cick the "get output" button

Then, you have to filter this file and keep only the lines with:

• repFamily = 'Alu' OR 'L1' OR 'SVA'
• or repName like 'HERV%' OR 'SVA%'