Add Manta support for structural variant prediction

[jonasscheid]

Description of feature

The pipeline should also be able to predict putative Neo-epitopes based on structural variants (SV). Currently we only support SNVs and small indels. Predicting Neo-epitopes based on SV could reveal further therapy targets, e.g. deriving from gene-fusions. A common SV annotation tool is Manta

[qbicStefanC]

That feature would be indeed needed, especially for pre-clinical individualized trials we are involved into from time to time. I guess one could make use of additional evidence from RNA-Seq whether the fusion genes is indeed expressed, in order to confirm the importance of the variant.

[christopher-mohr]

That feature would be indeed needed, especially for pre-clinical individualized trials we are involved into from time to time. I guess one could make use of additional evidence from RNA-Seq whether the fusion genes is indeed expressed, in order to confirm the importance of the variant.

Hi Stefan, I am not sure if Jonas had a closer look into this already. At the moment it is not entirely clear to me what would be needed to support this. On a high level I assume:

• parsing functions for Manta-annotated variants
• function(s) to incorporate structural variants accordingly