1.9.0

• Updated to latest versions of htsjdk and picard
• Separated breakpoint and single breakend filtering logic
• Only reporting assembled single breakends when single breakend reporting is enabled
  • Configurable using the variantcalling.callUnassembledBreakends setting
• Added BEIDL, BEIDH VCF INFO attributes to enable unambiguous reporting of SV chains linked through assembly
• Removed deprecated INPUT_NAME_SORTED command line parameter

1.8.1

Bug fix release:

• #156 unanchored assemblies are no longer being scored as 0
• #156 unanchored assemblies no longer cause QUAL breakdowns to be reported as NaN
• Strand bias now only calculated from read support since read pair support is expected to be 100% strand biased

Note that #156 was introduced in 1.8.0. It is strongly advised to rerun all samples run with 1.8.0 with 1.8.1.

1.8.0

• #154 Assembly support is now restricted to the interval over which the evidence supports the assembly contig
  • Improves quality scores, read counts, and AF calculation for complex compound SVs with multiple breakpoint in close proximity
• #153 Implemented assembly pro-rataing
• Added Dockerfile to better support docker based environments
• Fixed crash when printing error message when calculating edit distance of an unmapped read

Note that due to changes in the assembly SAM tags generated by GRIDSS assemblies, pipelines upgrading from an earlier version will need to regenerate the GRIDSS assemblies to run the variant calling and annotation portions of the GRIDSS pipeline.

1.7.2

Minor bug release:

• #138 outputting "PASS" instead of "." in the VCF FILTER column output
• Now checking that the configuration file is readable if it has been specified
• Fixed AnnotateUntemplatedSequence bug causing output to always be written to the final output file even when it should have been written to a temporary file
• Throwing exception when matching input.sv.bam files are missing during assembly or variant calling
  • Prevents misconfigured pipelines from completing, but with terrible results

1.7.1

Minor bug fix release:

• Counting constituent reads when calculating assembly contribution to VF annotation

1.7.0

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
  • Work-around for samtools/htsjdk#1105

1.5.1

• Metrics no longer count duplicate reads by default

This fixes a bug with low RP qual scores for libraries with high duplication rates.

1.5.0

GRIDSS has been optimised for improved performance as part of a NGS pipeline. GRIDSS preprocessing steps can now be run earlier in the pipeline, completely avoiding some steps (such as re-sorting), and improving multi-core utilisation as, unlike the pre-processing steps, GRIDSS assembly and variant calling calling is fully multi-threaded.

• Added example of running GRIDSS in an NGS pipeline
• Added unix pipe support for all GRIDSS preprocessing utilities
• Removed support for multimapping alignment
• Bug fix: compound split read realignment now working for bwa
• Updated dependencies to latest versions

1.4.3

• Excluding inversion-like breakpoints from the variantCalling.minSize filtering as the actual event size is not known from just the single breakpoint

1.4.2

• allowing colons in contig names. Parsing ambiguities are resolved in favour of the contig:position notation. #87
• out of bounds kmers are now ignored (with log error message) instead of causing assembly abort #89
• Fixed missing root cause log message when assembly failure is due to inconsistent input data and not due to an actual assembly error
• Ignoring BEDPE records on contigs not found in the reference genome instead of crashing on them.
• Adding line number logging of BEDPE parsing errors
• Fixed BreakpointHomology out of bound error when breakpoint near contig bounds
• Using string for BEDPE score for consistency with bedtools
• Added AnnotateInexactHomologyBedpe command line tool
• Corrected example to use BEDPE 0-based positioning for start (but not end)