manta-1.1.0

This release includes the following feature enhancements and bug fixes:

• Improved the robustness of the stats generation module estimating fragment size distribution.
• Fixed the problem of inaccurate genotyping multi-junction events with multiply samples.
• Fixed the bug of ill-formatted DELs due to unknown size insertion component.
• Merged the previous RNA specific branch and updated the RNA mode configuration.
• There are also documentation, source format and library/build changes.

Full ChangeLog:

• Manta-677 Stats generation
  • Add a sampling buffer to skip regions with a large number of abnormal reads
  • Add a compiler flag to output fragment-size cdf in stats summary
• Sync shared library/build changes with strelka
• Scratch: Merge src formatting changes from strelka
• Docs: Update comments in automated TOC generation; Fix nonstandard markdown links
• MANTA-583 Document multi-junction handling
• MANTA-518 Add sample level check of genotyping for multi-junction events
• MANTA-486/[#57] clarify rna mode configuration/improve errors
• MANTA-436 Classify indels with unknown size insertions as insertions
• MANTA-304 Merge RNAMaster branch
  • RNA: Include some spliced reads in insert-size estimation
  • RNA: Include split-reads as evidence for imprecise translocations
  • RNA: Use proper-pair BAM flag for abnormal pair detection

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manta-1.1.0.centos5_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 5 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The manta-1.1.0.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.