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Detect genomic fusions from paired or single ended DNA-seq or RNA-seq data using FusionMap. FusionMap works by splitting reads into three parts, aligning the prefix and suffix reads, and detecting fusions by discordant alignment of the prefix and suffix. The most important parameters are minSeedLength (alpha) and maxAlignments (beta).

Notes: FusionMap does not appear to work with Mono 3+, so Mono 2.10.9+ should be used. On the first run, FusionMap may take a long time at "Thread number=N"; this is due to downloading and processing of the genome index.

Version 1.0
Bundle sequencing
Categories Short-read Sequencing
Authors Kristian Ovaska (kristian.ovaska@helsinki.fi)
Issue tracker View/Report issues
Requires FusionMap ; Mono (2.10.9+ or 2.11)
Source files component.xml function.scala
Usage Example with default values

We have FusionCaller component.


Name Type Mandatory Description
reads RegionSet Mandatory Sequencing reads in FASTQ/FASTA/BAM format (optionally gzipped). Data can either include all reads, or only unmapped reads after an initial alignment; the latter reduces FusionMap run time.
mates RegionSet Optional For paired-end sequencing, these are the mate reads in the same format as primary reads.


Name Type Description
fusions CSV Fusion table. See column descriptions.
fusionReads BAM Fusion reads. Each read has been cut into two parts, which align to different locations.


Name Type Default Description
fusionMapPath string "" Path to FusionMap installation, i.e., the directory that contains bin as a subdirectory. This directory must be writable by the user. If the parameter is empty, the environment variable FUSIONMAP_HOME is used.
geneModelName string "Ensembl.R73" Code of the gene model in Array Suite nomenclature. Only used for RNA-seq.
maxAlignments int 1 Maximum number of read end alignments (beta in the FusionMap article). Range: 1 to 5.
memoryGB int 8 An estimate for memory usage by FusionMap. Only used in a cluster environment. For the human genome, 7-8 GB are needed.
minSeedLength int 25 Minimum length of a seed read (alpha in the FusionMap article). If 0, the length is computed using Min(25, Max(17,floor(ReadLength/3))).
mismatchPercentage int 8 Percentage (0 to 100) of allowed mismatches in alignment of reads.
monoExec string "" Path to Mono executable, if not on path. Example: /opt/mono/bin/mono.
referenceName string "Human.B37.3" Code of the reference genome in Array Suite nomenclature.
rna boolean true If true, data are from RNA-seq. If false, data are from genomic DNA-seq.
threads int 4 Number of threads used by FusionMap.

Test cases

Test case Parameters IN
case1_pe (missing) reads mates fusions (missing)
case2_se properties reads (missing) fusions (missing)


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