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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