2.7.3

• #276 driver script: directory creation failure now causes immediate termination
• Fixed crash error in somatic filtering script arg parsing
• Removed unnecessary error message

2.7.2

• Centre-aligning nominal call positions #266
• Improved repeat-kmer assembly performance from O(n^2) to O(n log(n))
• Fixed hang during assembly error recovery
• Fixed issue with high samtools memory usage during sorting steps
• Updated somatic filtering script
  • Added gridss.min_direct_read_support somatic filtering parameter (default: 1 read)
  • Changed minimum reported event size to 8bp to match GRIDSS default minimum
  • Renamed somatic tumour variant allele fraction field from BPI_AF to TAF
  • Renamed the names of some somatic filters to improve consistency
  • Fixed bug with simple somatic inversion detection breakpoint pairing logic (was not using correct QUAL score)
  • Added optional output plots to somatic filtering script

2.7.1

Reverted #266 changes to due crash

2.7.0

• Now reporting centre of any imprecision interval or microhomology as the nominal call position #266
• Switched from sambamba to samtools due to potential multithreaded sambamba instability #274
• gridss_annotate_insertions_repeatmasker.R no longer crashes when there are no records to process #256
• gridss_annotate_insertions_repeatmasker.R no longer requires NCBI style contigs #268
• IdentifyVariants no longer hangs if the input BAM is malformed #267
• /usr/bin/time output more verbose
• /usr/bin/time no longer required
• Fixed out of memory error during assembly gridss.SoftClipToSplitReads occuring on some data set

Note: binary removed due to crash bug. Use 2.7.1

2.6.3

This release add job scheduling support, improves assembly error debugging, and bug fixes.

• Added support for distributing assembly work across multiple nodes
  • Use the --jobindex and --jobnodes nodes parameters to distribute the work
  • Added examples/torque_example.sh
• Fatal assembly errors now generate a zip file containing the minimal data required to reproduce the issue. This file includes the following:
  • input file metrics
  • reads in the assembly graph at time of failure
  • reference genome. All regions not relevant to the failure are masked (replaced with N)
  • configuration file (if used)

Bug fixes/minor enhancements:

• Fixed assembly error (#260)
• Added checks to ensure assembly and variant calling have same inputs (#261)
• cohort scripts updated to match driver script (#240)
• SoftClipToSplitReads now writes temporary files to the correct directory (#250)
• Forcing C locale to prevent locale-based parsing errors due to number formatting (#253)
• Downgraded getopt failure to warning (#251)
• Added --picardoptions to expose standard command line options (#254)
  • Useful options include VALIDATION_STRINGENCY=LENIENT and COMPRESSION_LEVEL=0. See https://broadinstitute.github.io/picard/command-line-overview.html
• Removed PON generation script as it's been replaced by gridss.GeneratePonBedpe
• Fixed SoftClipToSplitReads duplicating SAM headers when using external merge
• Made terminal sambamba steps idempotent (#255)
• Exposing assembly read name prefix in assembly.contigNamePrefix configuration file parameter (#182, #261)
• Forcing assembly reinitialisation when unsupported assembly encountered

2.6.2

• Added command line option for SoftClipToSplitRead to perform sorting and merging externally
• Converted SoftClipToSplitRead sort and merge steps to sambamba call.
  • Fixes #247 out of memory error
  • Improves wall clock time

2.6.1

Bug fix release

• Only unrecoverable assembly errors will raise an error #237 #242 #244
• GRIDSS should no longer filter out small DUPs with long homology #243
• Driver script -labels argument no longer broken #245
• explicitly checking for non-null read pairing statistics when a record is flagged as paired #239

The simple somatic filtering script example/somatic.R has been removed. gridss_somatic_filter.R is a much more comprehensive script and should be used instead.

2.6.0

Somatic Calling

GRIDSS now has an offical tumour/normal somatic SV post-processing script.
This script has been developed for the Hartwig Medical Foundation cohort and is optimised for high quality sequencing data (40x normal, 100x tumour, ~500bp library fragment size, HiSeqX10/NovaSeq). It has been successfully used for clinical patient reporting in over 4,000 WGS patient samples.

The Hartwig hg19 GRIDSS panel of normals (PON) used in the somatic filter script can be downloaded from https://resources.hartwigmedicalfoundation.nl/.

Script	Description
scripts/gridss.sh	gridss driver script. Use this to run GRIDSS
scripts/gridss_somatic_filter.R	GRIDSS tumour/normal somatic filtering script. Run this script on the GRIDSS output.
scripts/libgridss.R	library used by gridss_somatic_filter.R
scripts/gridss.config.R	somatic filtering configuration used for the Hartwig cohort
gridss_annotate_insertions_repeatmaster.R	adds RepeatMasker annotations for VCFs annotated with gridss.AnnotateUntemplatedSequence

New docker images

• A new GRIDSS docker image has been created. It will be available on Docker Hub as gridss/gridss:2.6.0 shortly.
• A new combined GRIDSS/PURPLE/LINX docker image has been created. This docker image contains a stand-alone version of the Hartwig SV/CNV pipeline. It will be available on Docker Hub as gridss/gridss-purple-linx:latest shortly. Reference data required by this pipeline (including the GRIDSS PON) will be downloadable from https://resources.hartwigmedicalfoundation.nl/.

A GRIDSS/PURPLE/LINX bioarvix preprint will be posted soon.

Bug fixes

• #213 also excluding indel assemblies from contributing to support interval

2.5.2

This release fixes a crash when performing viral sequence annotation

• Fixed crash in gridss.AnnotateUntemplatedSequence when annotation sequence does not match reference sequence

2.5.1

Mostly bug fixes and driver script changes:

• Fixed log message error causing premature assembly safety mode abort
• Relaxing input BAM sort order checks to only require correctly sorted according to SAM file sort ordering
• Reducing memory usage by skipping directed evidence re-sorting when performing assembly
• Driver script tweaks:
  • #232 using "sambamba -n" for sorting for compatibility with older versions of sambamba
  • #233 Using 4g for entry points that do not use the --jvmheap option
  • Added bash version to driver script output
  • Using -Xms to test max memory usage up-front