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manta-v1.5.0
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@x-chen x-chen released this 13 Nov 20:12
· 139 commits to master since this release
v1.5.0
a922b74

v1.5.0 - 2018-11-12

This is a major update from v1.4.0, featuring improved precision and stability, a new configurable option of overlapping pair reads, and a few bug fixes. VCF representation is improved by introducing a couple of new filters and representing inversions as two breakend records.

Please note the changed format of inversions in the output VCF files. A supplementary script is provided that can be applied to Manta's output VCF files to reformat inversions into single inverted sequence junctions, which was the format used in earlier versions than this release. The details are described in the section "Inversions" of the Developer Guide.
https://github.com/Illumina/manta/tree/master/docs/userGuide#inversions

Added

  • Add a configurable option to allow overlapping pairs to be used as evidence (MANTA-1398)
    • The option is available in the configure file configureManta.py.ini

Changed

  • Change SV candidate contig aligners to improve precision (MANTA-1396)
    • Change contig aligners such that variant occurrences are more heavily penalized.
  • Fix multi-junction nomination (MANTA-1430)
    • Complex events with more than two junctions are no longer nominated as a group
    • Fix the problem of duplicate detection of the same SV candidate
  • Add index to ensure uniqueness of evidence bam filenames (MANTA-1431)
    • It solves the potential problem of name conflicts for evidence bams if the input bam files have the same name while located in different directories.
  • Change filters for easy interpretation of multi-sample germline variant vcf (MANTA-1343)
    • Add record-level filter 'SampleFT' when no sample passes all sample level filters
    • Add sample-level filter 'HomRef' for homogyzous reference calls
    • No more sample-level filter will be applied at the record level even if it applies to all samples
  • Change representation of inversions in the VCF output (MANTA-1385)
    • Intrachromosomal translocations with inverted breakpoints are now reported as two breakend (BND) records.
    • Previously they were reported in the VCF using the inversion (INV) allele type.

Fixed

  • Fix the bug of stats generation with short reference sequences (MANTA-1459/[#143])
  • Fix the evidence significance test in the multi-sample calling mode (MANTA-1294)
    • This issue previously caused spurious false negatives during the multi-sample calling mode. The incidence rate of the problem tended to increase with sample count.

manta-1.5.0.centos6_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 6 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The manta-1.5.0.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.

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