manta-0.21.0

Primarily germline calling improvements:

• Added a new filter for ambiguously mapped contigs.
• Assembly read selection for insertions (and to a lesser degree) all variants has been greatly improved,
• Minor assembler and somatic call filtering fixes.

manta-0.20.1

v0.20.1

• Lower default min candidate size to 8

v0.20.0

• MANTA-136 turn on conservative large insertion calling
• MANTA-126 multi-junction SV scoring
• MANTA-131 improve large somatic sv specificity with expanded
  supporting evidence search
• RNA: track candidate orientation

manta-0.19.0

• MANTA-127 RG based insert stats (default off)
• MANTA-128 Improved pair orientation estimation and error checks
• Improve fusion specificity in RNA-Seq mode
• MANTA-125 add experimental large insertion calling (default off)
• MANTA-125 add tier2 permissive split score to reduce small somatic
  FP deletions
• MANTA-125 add tier2 chimera rate to reduce somatic FP calls

manta-0.18.0

• MANTA-125 modify pair weight for small SVs
• MANTA-120 Improve stability of SV scoring as a function of read length

manta-0.17.0

• Filter SA split read segments by MAPQ value
• MANTA-116 better handle BWA-mem SA split-reads for inversions
• MANTA-118 static libstdc++ for gcc 4.5+

manta-0.16.0

• MANTA-117 add somatic quality score
• fix SA tag parsing
• MANTA-27 accept bam/fasta filenames with spaces

manta-0.15.0

• MANTA-108 combine clip/semi-aligned evidence detection, don't detect
  overlapping reads as assembly evidence
• MANTA-98 make fewer bam scans during scoring
• MANTA-106 add high depth limit to candgen and assmbler
• MANTA-75 Better match reads to SV candidates to improve
  runtime and lower repeat observations (part 2)
• MANTA-105 filter poorly supported candidates to reduce per-edge compute time
• MANTA-103 fix issue in RNA and WES modes introduced by MANTA-99

manta-0.14.0

• MANTA-102 filter calls with high MQ0 fraction
• MANTA-99 add high-depth graph filter to improve FFPE runtime
• MANTA-100 allow for neighbouring variants during assembly
• MANTA-83 sort vcfs in bam chrom order
• MANTA-96 Keep matching read pairs after candidate generation
  read buffer fills
• MANTA-89 Use semi-mapped read pairs to improve germline/somatic
  classification.
• MANTA-92 Add edge runtime performance log
• MANTA-75 Better match reads to SV candidates to improve
  runtime and lower repeat observations
• MANTA-85 Increase uniformity of tags in vcf output

manta-0.13.2

Documentation update:

• This release includes a first complete pass at the installation and user guides. The variant call output should be identical to manta-0.13.1

manta-0.13.1

Bugfix release for manta-0.13.0

• MANTA-81 Fix small indel somatic false negatives introduced
  in MANTA-63
• MANTA-80 Additional workflow options: run subsections of the
  genome, finer task parallelization control and merge multiple
  input BAMs per sample.