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Manta (Gene Fusion Caller)

Manta calls gene fusions from mapped paired-end sequencing reads. Manta identifies candidate fusions from discordant pair and split-read alignments, and then it performs local assembly and realignment to refine candidates.

The Manta workflow is followed by RNA-specific filtering and scoring, which is based on the following:

• Read counts across the fusion and alignment qualities.
• Genome-wide realignment of fusion contigs to filter candidates that a local alignment elsewhere in the genome can explain.
• Length of coverage around the breakpoints, indicating presence of stable fusion transcripts.

For more information, visit github.com/Illumina/manta.