2022_11

November 2022 release:

• VcfAnnotateConsequence: implemented multi-threading, added much more tests and fixed several bugs.
• NGSDExportSamples: added filters for HPO terms and ancestry.
• NGSD:
  • Added version number to table 'gene_transcript'.
  • Updated tissue list in table 'sample'.
  • Added comment field in table 'user'.
  • Added DRAGEN as caller in table 'sv_callset'.

Note: Please do not use the auto-generated 'Source code' packages - they will not work!

2022_10

October 2022 release:

• SeqPurge: improved CPU usage and scaling in multi-threaded mode.
• BedCoverage: added 'threads' parameter and removed 'dup' parameter.
• BedCoverage: now always works in panel mode.
• BedCoverage: added parameter to clear previous annotations.
• BedLowCoverage: added 'threads' parameter.
• BedHighCoverage: added 'threads' parameter.
• CfDnaQC: added 'threads' parameter.
• HgvsToVcf: added parameter for maximum sequence length.
• MappingQC: fixed support for non-human genomes.
• SampleGender: Ignoring duplicate, secondary and supplementary alignments in methods 'xy' and 'sry' now.
• RohHunter: updated documentation.
• VcfToTsv: Added support for streaming.
• Added tools: VcfToBed, TsvToQC.
• NGSD:
  • Added mechanism to protect the production database from being deleted with init() accidentally.
  • Updated transcript biotypes to Ensembl 107.
  • Added more tissue types to sample table.
  • Added 'archived' flag to project table.
  • Added fields for manual curation of variants to germline report configuration tables.

Note: Please do not use the auto-generated 'Source code' packages - they will not work!

2022_07

Juli 2022 release:

• VcfAnnotateFromVcf: refactoring of command line parameters and updated documentation.
• SampleSimilarity: changed number of SNPs for BAM mode, MODIFIER impact variants are now ignored in GSvar mode to make scores more similar between exomes and genomes, updated documentation.
• MappingQC: added metrics for uniformity of coverage in WGS mode.
• HgvsToVcf: Added handling of unnecessary sequences in 'delins', added support for dup/del with trailing sequence.
• VcfSort: files without FORMAT/SAMPLE columns are can now be processed without adding the column.
• VcfLeftNormalize: improved runtime when 'stream' parameter is not used.
• added tools: VcfAnnotateHexplorer, HgvsToVcf, VcfAnnotateConsequence
• NGSD:
  • transcript: added biotype, MANE Select flag, MANE Plus Clinical flag, Ensembl canonical flag.
  • variant: removed 1000g AF.
  • sample: added patient identifer, added tissue enum.

Please do not use the auto-generated 'Source code' packages - they will not work!

2022_04

April 2022 release:

• general: updated default genome build from 'hg19' to 'hg38' for all tools that require genome builds.
• added tools: BedLiftOver, BedpeSort, VcfAnnotateFromBigWig.
• NGSD:
  • user: added user type enum value 'restricted_user' and associated table 'user_permissions'.
  • sample: added sample type enum value 'cfDNA'.
  • sample: added field 'tissue'.
  • added table: 'variant_literature' for publications associated with a variant.
  • sv_deletion/sv_duplication/sv_insertion/sv_inversion/sv_translocation: added field 'genotype'.

Please do not use the auto-generated 'Source code' packages - they will not work!

2021_12

December 2021 release:

• VcfFile: fixed crash when VCF contains position 0.
• VcfAnnotateFromVcf: fixed error handling (seg-fault of error in worker thread occured).
• VariantFilterAnnotations: Added filter for variants with splicing effect.

Please do not use the auto-generated 'Source code' packages - they will not work!

2021_09

September 2021 release:

• GenePrioritization: Performs gene prioritization based on list of known disease genes and a PPI graph.
• GraphStringDb: Creates simple representation of String-DB interaction graph.
• VcfCheck: improved checking of empty INFO column
• VcfAnnotateFromBed: added multithread support
• VcfAnnotateFromVcf: improved memory useage
• MappingQC: added support for cfDNA samples, improved support for RNA
• NGSD:
  • removed 'gene' and 'variant_type' columns from 'variant' table
  • added 'germline_het' and 'germline_hom' columns to 'variant' table
  • added method 'shallow WGS' to 'variant_validation' table

Please do not use the auto-generated 'Source code' packages - they will not work!

2021_06

June 2021 release:

• General: Improved GRCh38 support in several tools.
• General: Using BGZIP for compressed VCFs now to allow indexing them with tabix.
• VcfAnnotateFromBed: Made separator configurable; Added check for separator in source BED file; Fixed broken output VCF if input has no FORMAT column.
• VcfAnnotateFromVcf: Fixed crash in VCF header parser.
• NGSDExportSamples: Added ancestry column.
• SampleAncestry: Improved runtime and memory use.
• SampleGender: Improved runtime for algorithm 'hetx'.
• SomaticQC: Added support for mutect2.
• NGSD:
  • Added disease status 'Unclear' to table 'sample'.
  • Added table 'processed_sample_ancestry'.
  • Added percent occupied to 'runqc_lane' (for Illumina NovaSeq).

Please do not use the auto-generated 'Source code' packages - they will not work!

2021_03

March 2021 release:

• SeqPurge: fixed bug that could cause hanging in case of currupt input data.
• VcfLeftNormalize: added option to steam the VCF if no compression is used.
• ReadQC: can now merge and write input FASTQ files.
• CnvHunter: is now deprecated - use ClinCNV instead.
• BamClipOverlap: Fixed handling of reads with insertion-only CIGAR.
• SampleSimilarity: improvements speed and memory usage.
• MappingQC: Added metrics for GC/AT dropout and homogeneity of coverage.
• NGSD:
  • Added pseudogene-gene relation table
  • Added more sample relations (twins, cousins, ...)
  • Added gap table

Please do not use the auto-generated 'Source code' packages - they will not work!

2020_12

December 2020 release:

• Added CRAM support.
• NGSD:
  • Added table for secondary analyses (trio, multi, somatic)
  • Added support for studies, which can include samples from serveral projects.

Please do not use the auto-generated 'Source code' packages - they will not work!

2020_09

September 2020 release:

• Added tools: FastqDownsample, BedpeAnnotateCnvOverlap, BedpeFilter, VcfCalculatePRS
• Added output compression level parameter to: FastqAddBarcode/FastqConvert/FastqExtract/FastqTrim/PERsim/VariantFilterRegions/VcfLeftNormalize/VcfSort.
• VariantFilterAnnotations/GSvar: Added filter 'somatic allele frequency'.
• NGSD:
  • Added preferred transcripts information
  • Added sample relations 'tumor-cfDNA' and 'same patient'
  • Added variant validation for CNVs/SVs (before only for small variants)

Please do not use the auto-generated 'Source code' packages - they will not work!