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general improvements in sensitivity for small events
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@brentp brentp released this 15 Oct 15:38
· 61 commits to master since this release
v0.2.1
a7e1b8c

this release was driven by feedback from Dave Larson (@ernfrid) and Ira Hall's group. It results in improved sensitivity for smaller events (at a small cost of specificity). It also fixes a bug with the duphold runner.

v0.2.1

  • fix bug in smoove duphold for samples > threads that resulted in stalling
  • smoove is now more discerning about reads that are soft-clipped on both ends as
    these could be due to inversions. if a read is not flipped relative to its mate
    and it is soft-clipped on both ends, it is still removed.
  • in some cases reads with a large NM (mismatches) were not filtered because they
    had an unexpected type (uint8). smoove now checks more types and for some bams
    will remove more records which improves specificity.
  • smoove will now be more conservative with NM counting. an insertion of 7 bases
    is counted as an NM of 7. smoove will now correct this to an NM of 1 so it counts
    the number of events rather than the number of bases of each event.
  • simplify rules for filtering and make them less strict.
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