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openvax / neoantigen-vaccine-pipeline

Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines
Apache License 2.0
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Add chimeric alignments to STAR #144

Open iskandr opened 5 years ago

iskandr commented 5 years ago

Since Manta does not do realignment on RNA it relies on STAR to do chimeric alignments.

We need to add --chimSegmentMin 30 to the STAR alignment parameters (requiring each part of a fusion to be at least 30bp long)