Manta
Manta calls structural variants (SVs) from mapped paired-end sequencing reads. Manta discovers candidate SVs from discordant pair and split-read alignments, followed by local assembly and realignment to refine candidates.
The app uses Manta on RNA-seq data to detect gene fusions in combination with STAR, which appear like translocations in the RNA alignments. The Manta workflow is followed by RNA-specific filtering and scoring, which is based on the following:
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Read counts across the fusion and alignment qualities. |
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Genome-wide realignment of fusion contigs to filter candidates that can be explained by a local alignment elsewhere in the genome. |
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Length of coverage around the breakpoints, indicating presence of stable fusion transcripts. |
For more information, see https://github.com/Illumina/manta.
RNA-Seq Alignment v1.0 Online Help