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hall-lab / svtyper

Bayesian genotyper for structural variants
MIT License
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(WIP) Split order #49

Closed ernfrid closed 7 years ago

ernfrid commented 7 years ago

These changes do two things:

  1. Order the arrangement of split-reads, where the two halves are not on the same chromosome, by the location of the clipping.
  2. Count soft-clips as split-reads where the soft-clipped section of the reads is treated as not supporting the breakpoint, but of 0 quality. This allows the mapped portion of the read to support the breakpoint, assuming that the location of the soft-clipping event would do so.

I am still evaluating these changes, but wanted to get the code out there.