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1.0.0

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@d-cameron d-cameron released this 13 Dec 06:08
· 1312 commits to master since this release
v1.0.0
e74d307

GRIDSS 1.0.0 is available and is now truly a software suite with each step now a separate, independent tool.

  • Explicit support for (bowtie2-style) multi-mapping reads.
  • New set of command-line tools in the gridss namespace:
    • CallVariants (this replaces Idsv as the all-in-one wrapper tool)
    • CollectGridssMetrics
    • CollectCigarMetrics
    • CollectIdsvMetrics
    • CollectMapqMetrics
    • ExtractSVReads
    • ComputeSamTags
    • SoftClipsToSplitReads
    • IdentifyVariants
    • AnnotateVariants
    • AllocateEvidence
    • AnnotateReferenceCoverage
    • AnnotateInexactHomology
  • Intermediate files now use the standard SAM tags and are much more useful for variant visualisation
  • Improved parallelisation
    • Parallelisation is no longer per chromosome and is now performed of arbitrarily sized genomic intervals (1Mb by default)
    • Variant identifiers are now deterministic
  • Split read handling is now symmetrical (no more RSR in the output file)
    • Assemblies still track the breakend from from which the contig was assembled
  • Indel-containing reads are now tracked separately to split reads
  • Improved support for single-end sequencing

Be sure to check out the README file and the updated examples for the new command line syntax.

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