Change log pipeline 31

Features

  • Pipeline version naming changed to match workbench version.

  • Annotation | Ensembl Variant Effect Predictor (VEP) updated to version 108

    • Refseq transcripts updated to version 110

    • The following effect modifications are updated in Filters > Severity > Simple mode

      • New effect types: splice_donor_5th_base_variant, splice_donor_region_variant, splice_polypyrimidine_tract_variant, start_lost, start_retained_variant

      • Modified effect types:

        • nc_transcript_variant ==> non_coding_transcript_variant

        • nmd_transcript_variant ==> NMD_transcript_variant

        • non_coding_exon_variant ==> non_coding_transcript_exon_variant

      • High severity CNV duplication calculation was expanded to include splice_polypyrimidine_tract_variant_, coding_sequence_variant & intron_variant&_feature_elongation in the severity calculation

  • Added support for DRAGEN Expansion Hunter's latest default catalog of 60 pathogenic STR loci (including 30 from gnomAD).

  • Added support for DRAGEN 4.0 for VCF cases (with disabled Machine Learning pipeline).

  • Labs running small panels can define gene list threshold below which case will deliver even without AI Shortlist results.

Bug Fixes

  • AI Shortlist | In a previous version, the algorithm for defining compound heterozygous variants was broken for pedigrees with additional samples. There is now support for compound heterozygous variants in any pedigree in the Autosomal Recessive - Compound Heterozygotes Inheritance Filter and Auto Analysis User Filter.

  • ACMG Automation | SNVs | Automatic PM5 ACMG tag calculation for SNVs is now more precise.

  • Annotation | REVEL | Updated REVEL scores with GRCh38 positions.

  • Annotation | mtDNA | APOGEE and MitoTIP mtDNA variant missense prediction scores are displayed again.

  • Annotation | ClinGen | Consistent annotation for CNVs classified as Uncertain by ClinGen in GRCh38 cases.

  • Variant Page | Format of dbSNP link is fixed.

  • Population Statistics | Fixed the issue with CNV population data being displayed incorrectly in some cases.

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