State-of-the-art structural variant calling: What went conceptually wrong and how to fix it?

摘要: Structural variant (SV) calling belongs to the standard tools of modern bioinformatics for identifying and describing alterations in genomes. Initially, this work presents several complex genomic rearrangements that reveal conceptual ambiguities inherent SV representations state-of-the-art callers. We contextualize these theoretically as well practically propose a graph-based approach resolving them. Our graph model unifies both strands using concept skew-symmetry; it supports genomes general pan specific. Instances our are inferred directly from seeds instead commonly used alignments conflict with various types reported here. For yeast genomes, we compute adjacency matrices demonstrate they provide highly accurate descriptions one genome terms another. An open-source prototype implementation is available under MIT license at https://github.com/ITBE-Lab/MA.