I'm having some trouble differentiating between CNV, split reads and read pairs and how each one elucidates the presence of a structural variation, say deletion.

Given a reference and donor sequence, I'd like to see a visual depiction (a link to a reference would be welcome) of a deletion event being detected by each of the above read types. In particular, I'd like to see how each of the read types detects the deletion event itself (i.e structural variant type) and its location (i.e the breakpoint junction).

Bonus points if it also includes some of the other common structural variants like inversion, duplication and insertion.

  • $\begingroup$ Welcome to Bioinformatics! This question need more information to be possible to answer. What papers did you read or which tools aren't helpful (and why not?)? Many thanks! $\endgroup$
    – llrs
    Nov 7, 2018 at 13:40


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