text: user10791: 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
  
  user11883: A structural variant is an inversion, deletion, duplication, or translocation. A "breakend" 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.
  
original_text: 10791: <p>I'm reading the Manta <a href="https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md" rel="nofollow noreferrer">User Guide</a>
  → it is a method to discover structural variants and indels from next generation sequencing data.</p>
  <p>The word 'breakend' is used in several contexts</p>
  <p>I have searched for a definition in <code>duckduckgo</code>, <code>qwant</code> and <code>google</code> but have not found a concise definition.</p>
  <p>Thanks for you help</p>
   11883: <p>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.  <em>Nature Review Genetics</em> 2011) may help you understand: <a href="https://www.nature.com/articles/nrg2958" rel="nofollow noreferrer">https://www.nature.com/articles/nrg2958</a></p>
  <p>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: <a href="https://academic.oup.com/bioinformatics/article/28/18/i333/245403" rel="nofollow noreferrer">https://academic.oup.com/bioinformatics/article/28/18/i333/245403</a></p>
  <p><strong>Specific example:</strong> 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 (<a href="https://en.wikipedia.org/wiki/Philadelphia_chromosome" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/Philadelphia_chromosome</a>). The genomic position of the location where chr9 turns to chr22 is called the breakpoint. The positions on chr9 and chr22 are the breakends.</p>
  