Up: Component summary

FusionCaller

Gene fusion detection.

The component includes 6 different tools (FusionCatcher, ChimeraScan, deFuse, SOAPfuse, EricScript, and STAR-Fusion) for gene fusion detection from RNA-Seq paired-end input reads. It is suggested to use the very raw reads without trimming since the tools perform their own trimming and quality filters on the reads in the early stages of their pipelines.

Before run the compenent install the fusion detection tool you want to use and create its genome database with the respective installation scripts in $ANDURIL_HOME/bundles/sequencing/lib/install_scripts/.

If you have your own installation of any of the callers, add a link to it in $ANDURIL_HOME/bundles/sequencing/lib/.

The component requires the dependecies that the single fusion detection tool require (see the official documentation of each tool for more information).

Dependencies:

--------------> FusionCatcher (https://github.com/ndaniel/fusioncatcher) Python 2.7.6 (>=2.6.0 and < 3.0 is fine)

--------------> deFuse (https://bitbucket.org/dranew/defuse) To build the deFuse toolset you must have the boost c++ development libraries installed. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH). Additionaly it requires: R, Rscript, R ada package, bowtie, bowtie-build, bwa, blat, faToTwoBit, gmap, gmap_build installed and present in $PATH. To install the ada package run R, then at the prompt type install.packages("ada")

--------------> EricScript (https://sourceforge.net/projects/ericscript) Perl Requires R, ada package, bwa, Bedtools, Seqtk, BLAT installed and present in $PATH.

--------------> ChimeraScan (https://code.google.com/archive/p/chimerascan/) Python >=2.6 Additionaly it requires: Pysam, bowtie, bowtie-build installed and present in $PATH.

--------------> SOAPfuse (https://sourceforge.net/projects/soapfuse) Perl >=5.8.5

--------------> STAR-Fusion (https://github.com/STAR-Fusion/STAR-Fusion/wiki) Requires: - STAR https://github.com/alexdobin/STAR - samtools http://www.htslib.org/download/ - possibly some non-standard Perl modules - see below: A typical perl module installation may involve: perl -MCPAN -e shell install DB_File install URI::Escape install Set::IntervalTree install Carp::Assert install JSON::XS install PerlIO::gzip

Inputs

Outputs

Parameters

Test cases