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sensitivity improvements

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@brentp brentp released this 06 Apr 18:00
· 116 commits to master since this release

NOTE: there is a change to svtyper that we found in evaluating smoove that will reduce the FPR from genotyping. Please update to svtyper>0.6.0 for best results.

v0.1.5

  • sensitivity increases for variants without split reads.
  • use a fixed length of 4 in merge (gives much better merging for smoove merge)
  • add new annotate command which takes a gff and annotates with gene names
  • increase max_reads argument to svtyper to reduce false negatives
  • remove QCFail and duplicate reads from split and disc.bams. This is now
    part of smoove but also fixed in lumpy_filter upstream.