2025_01

Changes:

• added tools: QcToTsv, TsvDiff
• removed tools: PERsim, SampleDiff, VcfMerge
• NGSD:
  • device: added type Revio
  • variant_classification/report_configuration_cnv/report_configuration_sv: renamed class R* to R
• BamToFastq: added flags -extend and - fix
• NGSDAnnotateSV: now only annotates overlapping pathogenic SVs in NGSD
• TsvSlice: add flag -rm
• VcfAdd: now contains all functionality of the removed tool VcfMerge
• VcfBreakMulti: Added correct handling of phased GT

Full Changelog at: 2024_11...2025_01

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

2024_11

Changes in release 2024_11:

• general: Added parameter --settings to all tools, which overrides the regular settings files
• new tools: FastaFromBam, FastaMask, TranscriptComparison, VcfStrip
• FastaInfo: added parameters -write_n and -write_other
• NGSDAddVariantsGermline: merged type-specific force parameters into one parameter -force
• NGSD:
  • Added variant classifcation R* to all classifcation enums
  • Added table report_polymorphisms

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

2024_08

Changes in release 2024_08:

• added tool: CnvReferenceCohort
• removed tool: NGSDMaintain (functionality now in GSvar NGSD maintainance dialog)
• NGSDExportSamples: added option -add_study_column
• NGSDSameSample: added option -include_bad
• NGSD: added new table runqc_ont

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

2024_07

Changes in release 2024_07:

• BedCoverage: improved runtime by using chromosomal sweep instead of random access (added parameter -random_access)
• BedHighCoverage: improved runtime by using chromosomal sweep instead of random access (added parameter -random_access)
• BedLowCoverage: improved runtime by using chromosomal sweep instead of random access (added parameter -random_access)
• VcfAnnotateConsequence: added support for RefSeq GFF file
• VcfFilter: added parameter -filter_clear
• NGSD:
  • kasp_status: added fields calculated_date and calculated_by.

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

2024_06

June 2024 release:

• new tools: NGSDExportIgvGeneTrack
• BamFilter: added parameter for maximum insert size
• NGSDAddVariantsGermline: now imports REs as well
• NGSDExportSamples: new paramters -only_with_small_variants and -add_lab_columns.
• SampleGender: new parameter -include_single_end_reads for long-read data.
• SampleSimilarity: new parameter -include_single_end_reads for long-read data.
• SampleSimilarity: new parameter -roi_hg38_wes_wgs to make WES, WGS and lrGS results more comparable.
• UpdHunter: new parameter -out_informative to write out a IGV track with informative variants.
• VcfCalculatePRS: new parameter -min_depth and support for variants that are to be imputed independent of the sample genotype.
• NGSD:
  • added tables for somatic SVs: somatic_somatic_sv_callset, somatic_sv_deletion, somatic_sv_duplication, somatic_sv_insertion, somatic_sv_inversion, somatic_sv_translocation, somatic_report_configuration_sv
  • added tables for repeat expansions: repeat_expansion, repeat_expansion_genotype, re_callset, report_configuration_re
  • processed_sample table: added boolean scheduled_for_resequencing to flag samples for resequencing to increase depth/coverage

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

2024_02

February 2024 release:

• new tools: NGSDExportIgvGeneTrack, VcfMerge, VcfSplit, BamExtract
• removed tools: CnvHunter
• NGSDSameSample: Added option '-include_merged'
• VcfFilter: Added options '-remove_non_ref' and '-no_special_chr'
• VcfCheck: Added check for main header line
• VariantRanking: using NGSD annotations by default now, skipping mosaic variants now
• SampleSimilarity: added parameter 'roi_hg38_wes_wgs'
• VcfLeftNormalize: now skips invalid variants

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

2023_11

November 2023 release:

• new tools: NGSDSameSample
• MappingQC: added long-read support
• NGSDExportGff: added parameter 'genes' to add/skip gene lines
• NGSDExportSamples: added parameter 'add_call_details' to export variant calling tools and dates
• VariantQC: added long-read support
• NGSD
  • Added 'small_variants_callset' table.
  • Added field 'classification' to 'somatic_vicc_interpretation' table.

2023_09

September 2023 release:

• new tools: VcfAnnotateMaxEntScan, SamplePath, NGSDImportGenlab, NGSDImportOncotree
• NGSDExportSamples: added '-add_dates' flag.
• VcfLeftNormalize: added flag '-right' to right-normaliazion.
• NGSD
  • Updated enums of 'sequencing_run' for NovaSeqX+ suppport.
  • Added 'year_of_borth, 'order_date' and 'sampling_date' to 'sample' table.
  • Added 'processing_modus' enum and 'batch number' varchar to 'processed_sample' table.
  • Added tables 'oncotree_term', 'oncotree_parent' and 'oncotree_obsolete'.

2023_06

June 2023 release:

• new tools: GenesToTranscripts, NGSDImportSampleQC, GenesToTranscripts, TranscriptsToBed, NGSDExportGff.
• BamToFastq: Added support for single-end.
• MappingQC: Added support for read QC.
• VcfToBedpe: Added support for Sniffles, cuteSV and dipdiff.
• FastqExtract: Added parameter 'long_read'.
• ReadQC: Added parameter 'long_read'.
• NGSDExportSamples: added parameters 'run_after' and 'no_normal'.
• NGSDExportAnnotationData: speed-up by parallelization.
• NGSD
  • Added 'side' enum to 'sequencing_run' table
  • Added 'germline_mosaic' to 'variant' table
  • Added 'hpo_obsolete' table with obsolete HPO terms
  • Refactoring of 'expression' and 'gene_expression' tables to speed-up queries

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

2023_03

March 2023 release:

• NGSDImportEnsembl: Update to support Ensembl 109
• RnaQC: Added target region to support targeted transcriptomics experiments
• NGSD
  • Added ncbi_id to gene table
  • Added folder_overrideto processed_sample table

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