manta-1.4.0

v1.4.0 - 2018-04-25

This is a major bugfix update from v1.3.2, featuring improved precision and vcf representation, in addition to minor user friendly improvements.

Changed

• Refine SV candidate filter to improve precision (MANTA-1310)
  • Change assessment of assembled SV candidate contigs such that indel occurrences near breakends are more heavily penalized and indel extension penalties are removed.
• Improve the accuracy of SV breakend position for precise calls (MANTA-1178)
  • Expand the reference sequence for the rare cases where a detected breakend is close to the reference end.
• Improve sensitivity for RNA calling (MANTA-1330)
  • Reduce the length of reference sequence to which an assembled SV candidate contig is aligned.
• Add strict checks and improve error message for BED regions of size less than one (STREL-865)
• Improve user guide to clarify meaning of the INV3/INV5 vcf INFO tags (MANTA-1305)
• Remove BND from vcf ALT field to comply with vcf spec (MANTA-1314)

Fixed

• Fix the off-by-1 bug for vcf HOMSEQ tag in certain variant types (MANTA-1311)
  • Due to position adjustment for certain breakends of inversions and duplications, HOMSEQ was off-by-1 for those variants.
• Fix a bug in breakend homology logic for large variants (MANTA-1313)
  • The breakend insertion was not considered previously when identifying breakend homology sequence.

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manta-1.4.0.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-1.4.0.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.