manta-0.26.0

• General:
  • Expand conditions where large insertion search and reporting is allowed.
  • Expand search around breakends for split read support at scoring phase (driven by RNA cases)
  • Remove discovery phase pair counts from all but candidate files (confusing because scored output PR counts should replace discovery estimates)
  • Support bwa-mem “-M” split read format
  • Filter large scale SV candidates without significant signal/noise based on noise rates in the target sample (dynamic noise thresholds for FFPE cases)
  • Correctly handle reads with N’s and low-qual bases during assembly input
  • Build system improvements for build auditing and VS Studio support
  • Improve handling for large event configuration
• Germline:
  • Filter large SVs with no read pair support.
• RNA:
  • Use short-fragments as fusion evidence instead of filtering out
  • K-mer reference mask accelerates RNA contig alignments

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The manta-0.26.0.release_src.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they are missing version numbers and build system changes to improve portability.