v7.2.1

What's Changed

• Re-enable long read alignment in report by @bartcharbon in #544
• 'multiple VIP' installer utility script by @dennishendriksen in #545
• Bump vcf-report 5.8.0 to 5.8.1 by @dennishendriksen in #546
• Update inheritance match node: gene must match by @dennishendriksen in #547

Full Changelog: v7.2.0...v7.2.1

v7.2.0

What's Changed

• FASTQ quality check and filtering by @bartcharbon in #536
• Installer improvements by @dennishendriksen in #540
  • Host all files in one place / do not rely on files hosted by third parties
  • Verify checksums of downloaded files
  • Option to host files on your own server
• Add hint to 'samples from different family' error by @dennishendriksen in #537
• Fix Java memory usage by @dennishendriksen in #538
• Workaround for Expansionhunter output missing SVTYPE by @bartcharbon in #539
• Fix #336 build.sh only works if ran from script directory by @dennishendriksen in #542
• Fix cuteSV workaround by @dennishendriksen in #541

Full Changelog: v7.1.0...v7.2.0

v7.1.0

What's Changed

• Support GRCh37 and T2T inputs via liftover by @dennishendriksen in #529
• gnomAD v4 by @dennishendriksen in #534
• Improved inheritance match annotations and reporting by @bartcharbon in #535
• Classify and filter short tandem repeat variants by @bartcharbon in #524
• Fix: crams not reaching the report by @bartcharbon in #526
• Fix: update (variant) feature types in annotation plugins by @dennishendriksen in #525
• Fix: normalize concatted gvcf to remove duplicates by @bartcharbon in #528
• Fix: bcftools sort --max-mem values by @dennishendriksen in #532
• Fix: reintroduce cuteSV workaround by @bartcharbon in #533

Full Changelog: v7.0.0...v7.1.0

v7.0.0

What's Changed

• Require GNU-based Linux by @dennishendriksen in #522
• Stop supporting GRCh37 by @dennishendriksen in #523

Full Changelog: v6.3.0...v7.0.0

v6.3.0

What's Changed

• Parallel fastq processing by @bartcharbon in #498
• ncER annotations by @bartcharbon in #504
• Sample decision tree improvements by @dennishendriksen in #512
• Update VKGL 202307 to 202311 by @dennishendriksen in #516
• Update ClinVar 20230910 to 20231104 by @dennishendriksen in #517
• Bump vip-report to 5.7.0 by @bartcharbon in #519
• Bump inheritance matcher 2.1.8 to 2.1.9 by @dennishendriksen in #520
• Add glnexus.WES preset DeepVariantWES_MED_DP by @dennishendriksen in #506
• Remove glnexus.WGS preset DeepVariantWES by @dennishendriksen in #506
• Fix sample sheet project validation by @dennishendriksen in #518
• Replace FTP with HTTPS downloads by @dennishendriksen in #507
• Update Nextflow 23.04.1 to 23.10.0 by @dennishendriksen in #515

Full Changelog: v6.2.0...v6.3.0

v6.2.0

What's Changed

• Manta joint SV calling by @dennishendriksen in #493
• DeepTrio variant calling for trios and duos by @dennishendriksen in #496
• Update classification trees: swap SV and gnomAD filter blocks in the tree by @bartcharbon in #486
• Run GADO once per project by @bartcharbon in #487
• Test runner: caching, parallelization, test selection, GIAB test cases by @dennishendriksen in #488 and #494 and #473
• Update annotation documentation by @dennishendriksen in #502
• Util scripts: create reference sequence mmi by @dennishendriksen in #492

Full Changelog: v6.1.1...v6.2.0

v6.1.1

What's Changed

• Validate that input contigs exist in reference by @dennishendriksen in #482
• Fix install.sh: download unzipped ref index files by @dennishendriksen in #485

Full Changelog: v6.1.0...v6.1.1

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