v6.1.0

What's Changed

• Additional sample validation rules by @dennishendriksen in #470
• Reintroduce deep variant by @bartcharbon in #460
• Change .g.vcf merge preset default to 'DeepVariant' by @dennishendriksen in #478
• Log test error messages to console by @bartcharbon in #474
• Fix #471 cram_str_straglr_call can produce unsorted vcf by @dennishendriksen in #472
• Fix ClinVar annotations with null values by @dennishendriksen in #484

Full Changelog: v6.0.2...v6.1.0

v6.0.2

What's Changed

• Fix #467 Report with long-read alignment hangs by @dennishendriksen in #468
• Fix #244 gnomAD and ClinVar annotations can be incorrect by @dennishendriksen in #463

Full Changelog: v6.0.1...v6.0.2

v6.0.1

What's Changed

• Fix create_inheritance.sh: update incomplete penetrance file path by @bartcharbon in #464
• Fix: gvcf workflow results might be invalid for multi-sample projects by @dennishendriksen in #465

Full Changelog: v6.0.0...v6.0.1

v6.0.0

What's Changed

New Features

• Short tandem repeat annotation for both short-read and long-read sequencing data
• AlphScore: AlphaFold2-based pathogenicity prediction score annotation for missense variants
• genomic vcf workflow gvcf
• Update vcf-inheritance-matcher 2.1.6 to 2.1.8 (see here)
  • Set inheritance match to 'missing' instead of '0' if gene inheritance patterns are unknown
  • Use only blood relatives in inheritance matching
• Update vcf-report 5.5.2 to 5.6.0 (see here)
  • Fix GADO default HC filter in default report template
  • Improved inheritance filters in default report template
• Update vcf-decision-tree-3.5.4 to 3.7.0 (see here)
  • Enable use of GADO and AlphScore fields in classification tree
• Restart Slurm process on certain errors
• Support .sam input in addition to .bam and .cram
• Validate input .vcf and .g.vcf contents
• Update VKGL annotations to 20230401 to 20230701
• Update ClinVar annotations 20230604 to 20230910
• Update HPO ontology to 20230822
• Update Clair3 v1.0.2 to v1.0.4 (see here)
• Update minimap2 2.24 to 2.26 (see here)
• Enable minimap2 soft-clipping

Bug Fixes

• Fix #405 Error if .cram doesn't contain reads for a chunk
• Fix #418 Multi-project handling of probands, HPO terms and pedigree
• Fix #419 Multi-project slice called too many times
• Fix #423 SV calling cannot detect translocations due to chunking
• Fix #428 Project samples can have different assembly and sequencing_method
• Fix #430 Variant calling can fail due to cram-to-bam slice-and-convert issue
• Fix #435 Succesfull pipeline execution if individual_id doesn't exist in VCF
• Fix #436 Input VCF index not created with HTSlib causes pipeline run failure
• Fix #437 Report can contain data of samples not in sample sheet
• Fix #439 cuteSV can fail based on ~ content on host machine
• Fix: GLnexus memory usage: stick to limits
• Fix: GADO uses same HPO as VIP
• Fix: do not mount apptainer home directory

Breaking changes

• vcf workflow does not accept .g.vcf files, use new gvcf workflow instead, see here
• configuration changes, see here for new parameter names and process labels

Full Changelog: v5.8.2...v6.0.0

v5.8.2

What's Changed

• Fix #432 annotate can fail with 'Failed to instantiate plugin GADO' by @dennishendriksen in #434
• Fix #431 'Chromosome blocks not continuous' error by @dennishendriksen in #433

Full Changelog: v5.8.1...v5.8.2

v5.8.1

What's Changed

• GADO predictions by @bartcharbon in #412 and #421
• CAPICE pathogenicity prediction improvements using gnomAD HN by @SietsmaRJ in #420
  • Default decision trees CAPICE thresholds updated, see validation data
• Fixed report VCF download in case of missing sample values by @dennishendriksen in #422

Full Changelog: v5.7.2...v5.8.1

v5.7.2

What's Changed

• Fix disable/enable cram feature by @bartcharbon in #414

Full Changelog: v5.7.1...v5.7.2

v5.7.1

What's Changed

• docs:describe relationship to other licences by @dennishendriksen in #410
• Use nextflow environment variables if already exist by @bartcharbon in #411
• bump vcf-report-5.4.0 to vcf-report-5.4.1 by @dennishendriksen in #413 that fixes molgenis/vip-report-vcf#26

Full Changelog: v5.7.0...v5.7.1

v5.7.0

What's Changed

• Short tandem repeat detection using Expansion Hunter by @dennishendriksen in #394
• Documentation improvementsby @bartcharbon in #404
• Automate documentation deployment by @bartcharbon in #402, #403 and #407
• Add option to enable/disable crams in report by @bartcharbon in #409
• Fix: workaround for N in REF of cuteSV by @bartcharbon in #406
• Fix: revert "gnomAD before annotSV" by @bartcharbon in #408

Full Changelog: v5.6.0...v5.7.0

v5.6.0

What's Changed

• Validate vcf after clair3 run by @bartcharbon in #381
• Fix #385 VEP out-of-memory workaround: replace bigWig with bed by @dennishendriksen in #384
• Fix #386 fastq/cram workflows do not validate params of subworkflows by @dennishendriksen in #387
• Fix #388 Replace Sniffles2 with cuteSV by @dennishendriksen in #382
• Update VKGL, ClinVar, Inheritance, HPO, AnnotSV by @dennishendriksen in #390
• Fix #391 concat_vcf input file name collision by @dennishendriksen in #392
• Change order of GnomadAF and AnnotSv in default tree by @bartcharbon in #393
• Fix awk command in annotSV workaround by @bartcharbon in #395
• Fix #389 samtools markdup can fail by @dennishendriksen in #396
• Bump vip-report to 5.4.0 by @bartcharbon in #398

Full Changelog: v5.5.1...v5.6.0