This software is intended to call fusion and exon-skipping events from raw sequencing data generated from human samples using the Twist Alliance CeGaT RNA Fusion Panel and sequenced on Illumina HiSeq/NovaSeq systems. Note that this software is not intended for installation on personal computers, and does not offer a graphical user interface. It is intended to be run as part of bioinformatics pipelines on compute infrastructure and its output files will need to be post-processed for interpretation by non-technical users.
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Fusion detection involves multiple steps that are performed automatically by our software package: First, reads are aligned using the STAR aligner (Dobin et al, Bioinformatics 2013) to the human reference genome hg19. After a first mapping pass, identified novel splice sites are integrated into the reference and a second pass mapping is performed. The resulting read alignments are analyzed by STARfusion (Haas et al, Genome Biol 2019) to detect fusion transcripts. We post-process the STARfusion output to correct for varying levels of read duplication, filter fusion calls to the intended panel target regions, and scan for transcript variants (e.g., MET exon 14 skipping) which STARfusion does not detect.