manta-0.26.2

Code portability and documentation update:

• Updated all build/installation and contributor guidelines
• Updated Manta user guide
• Added Travis CI configuration file for clang/gcc build and demo run
• Minor code edits to clean compile on OS X 10.9, CentOS 5,6,7, Ubuntu 12.04 and 14.04
• Updated demo: new dataset covers COSMIC HCC1954 variants, added test to verify expected output from demo run.

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manta-0.26.2.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-0.26.2.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.

manta-0.26.1

Minor bugfix release:

• Configuration process changed to remove python reflection, which was exhibiting infrequent but hard to reproduce failures.
• Fixed VCF header FileData to FileDate

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The manta-0.26.1.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.

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.

manta-0.25.0

This release primarily brings together some long-standing RNA and DNA logic forks. Split-read handling improvements from the RNA workflow should benefit DNA-Seq recall (esp for FFPE).

• RNA
  • parameter adjustments, additional vcf output, orientation fixes
• MANTA-187
  • treat split reads symmetrically to improve RNA fusion detection
  • detect split reads directly rather than via associated soft-clip sequence
  • exclude split reads from contributing to local assembly evidence

manta-0.24.0

Extensive runtime optimization and logging to handle several very difficult FFPE cases in practical time.

• MANTA-213 FFPE runtime optimization:
  • Recognize new BAM record format for fragments shorter than read length, prevent these reads from triggering assembly.
  • Improve insert size distribution estimation by including fragments shorter than read length.
  • Add new runtime instrumentation report for candidate generation
  • Add runtime summary to existing graph report
  • Reduce SW edit matrix size with short k-mer match bounds on ref seq
  • Improve graph noise filtration by testing specific region for evidence signal threshold
  • Use adaptive noise rates in hypoth gen step: background read anomaly rate is used to determine if signal is significant. Currently applies to small assembly candidates only.
  • Collapse redundant assembly candidates for small indels to single copy

manta-0.23.2

Backport stability fix to the v0.23.x branch:

• - [#6] Fix assertion caused by filtered graph edges on bin boundaries.

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manta-0.23.2.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-0.23.2.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.

manta-0.23.1

Added FFPE runtime improvements to v0.23.0:

• Filter out fragments shorter than read length
• Disable large insertion remote read search when running tumor/normal subtraction

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manta-0.23.1.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-0.23.1.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.

manta-0.23.0

• MANTA-200 Add filter for overlapping diploid calls which can't be explained as two haplotypes.
• MANTA-199 Fix low-frequency fragment/breakpoint mismatch (primarily an issue when large numbers of short ref contigs were used, eg. unplaced and unlocalized contigs)
• Add CRAM support for individual tools - still need a quick chrom depth estimator for full workflow CRAM support
• MANTA-185 remove transloc calls with neg position (from circular genome)
• [mantadev] #1 Fix SA split read breakpoint position
• MANTA-183 handle paired/single read mixture in input alignments
• MANTA-182 submit config on cmdline

manta-0.20.2

• MANTA-185 remove transloc calls with neg position (from circular genome)

manta-0.22.0

Changes since v0.21.0 primarily focus on further improvements to long insertion detection

• A new path-finding method for the assembler which reduces haplotype switching and early path termination
• Several related alignment and scoring changes have been added to support large insertion calling
• Manta now automatically produces a starling/strelka candidates file for sizes 50 and below, and provides a script for other size choices.