What is the exact definition of "breakend"? I'm reading the Manta User Guide
→ it is a method to discover structural variants and indels from next generation sequencing data.
The word 'breakend' is used in several contexts
I have searched for a definition in duckduckgo, qwant and google but have not found a concise definition.
Thanks for you help
A structural variant is an inversion, deletion, duplication, or translocation. A &quot;breakend&quot; is one endpoint of a structural variant. This paper (Alkan et al.  Nature Review Genetics 2011) may help you understand: https://www.nature.com/articles/nrg2958
The Manta paper and documentation seem sparse on diagrams. DELLY, another structural variant caller, has diagrams in their publication. Their paper may be more of use: https://academic.oup.com/bioinformatics/article/28/18/i333/245403
Specific example: Say you're sequencing a chronic myeloid leukemia (CML) tumor. You will likely find reads that half map to the ABL1 gene on chr9 and half map to the BCR gene on chr22 (https://en.wikipedia.org/wiki/Philadelphia_chromosome). The genomic position of the location where chr9 turns to chr22 is called the breakpoint. The positions on chr9 and chr22 are the breakends.