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@d-cameron d-cameron released this 21 May 00:25
· 1022 commits to master since this release
v1.7.0
e8e5ce1

Major update that includes multiple new features:

  • Added option to report single breakends
    • Uses VCFv4.3 notation
    • Set variantcalling.callBreakends = true in the configuration file to include breakends in the output VCF
  • Reads will be preferentially allocated to the variant supported by the assembly the read forms part of
  • Added the following fields to the VCF output:
    • SB: strand bias. 0 indicates all breakend-spanning reads are on the negative strand, 1 indicates all on the positive strand
    • BANSR/BANRP/BANSRQ/BANRPQ: counts/quality scores of split reads/read pairs whose breakend assembly does not support the same breakpoint.
    • VF: variant fragments supporting the breakpoint.
      • Avoids double-counting of SR+RP fragments and assembled/unassembled supporting reads.
  • Realigning assemblies and only including them when the realignment overlaps the originating assembly position #113
  • Extended default anchor length to 300bp to ensure anchor does not have worse mapping that constituent reads for libraries with longer read lengths
  • Added category support CIGAR to assembly output #114
    • Per category assembly support now requires read support on both size of the assembly breakpoint position
    • Fixes problem in which somatic SVs immediately adjacent to germline indels would be classified germline due to an assembly spanning both the indel and SV.
    • This is configurable by the variantcalling.requireAssemblyCategorySupport configuration file property
  • SoftClipsToSplitReads: re-adjusts split position after realignment to minimise edit distance. This prevents over-alignment of a longer fragment that has an imperfect homology to the other side of the split.
    • Enabled via the SoftClipsToSplitReads.READJUST_PRIMARY_ALIGNMENT_POSITON command line parameter.
    • By default, this is only performed on assembly contigs.
    • Fixed out of bound exception when split read overhangs reference sequence
  • Streaming SoftClipsToSplitReads bug fixes/enhancements:
    • Waiting for external aligner reader thread to actually complete before returning from flush()
      • Fixes issue with records missing from external aligner
    • Using MAX_RECORDS_IN_RAM to limit the number of outstanding alignment records when performing streaming alignment
      • Fixed out of memory error
  • Added gridss.AnnotateUntemplatedSequence entry point
    • Added BEALN to the output VCF. BEALN contains the potential alignment locations of breakend sequence reported by the aligner (bwa by default)
    • String list with each entry formated as chr:start|strand|cigar|mapq.
    • Depending on the alignment information available, strand and mapq may be empty.
  • Starting and ending anchors will no longer be added to a contig if they have inconsistent positions. Fixes #66.
  • variantcalling.minReads filter now uses VF annotation.
    • Fixes filtering bug in which minReads filter counted an assembly as a single read
  • Fixed crash error on assembly contigs with full-length homology
  • Changed missing R2/Q2 assertion to ignoring read so errors are not fatal.
  • Stripping sort order header from ComputeSamTags for compatibility with samtools sort
  • Fixed a race condition which resulted in a leaked file handle
  • #125 Using shorthand command line arguments for CreateSequenceDictionary
  • Updated to latest picard and htsdjk version
  • Added -gridss suffix to version number so it is clear that picard invocations are using the gridss jar.
  • Added replacement BasicFastqWriter that does not flush for every record written
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