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MITOMAP annotations support, Splice Junction Tracks and maintenance
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@northwestwitch northwestwitch released this 15 Apr 13:02
v4.32
a35a3d9
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Learn about vigilant mode.

[4.32]

Added

  • Load and show MITOMAP associated diseases from VCF (INFO field: MitomapAssociatedDiseases, via HmtNote)
  • Show variant allele frequencies for mitochondrial variants (GRCh38 cases)
  • Extend "public" json API with diseases (OMIM) and phenotypes (HPO)
  • HPO gene list download now has option for clinical and non-clinical genes
  • Display gene splice junctions data in sashimi plots
  • Update case individuals with splice junctions tracks
  • Simple Docker compose for development with local build
  • Make Phenomodels subpanels collapsible
  • User side documentation of cytogenomics features (Gens, Chromograph, vcf2cytosure, rhocall)
  • iSort GitHub Action

Fixed

  • Show other causative once, even if several events point to it
  • Filtering variants by mitochondrial chromosome for cases with genome build=38
  • HPO gene search button triggers any warnings for clinical / non-existing genes also on first search
  • Fixed a bug in variants pages caused by MT variants without alt_frequency
  • Tests for CADD score parsing function
  • Fixed the look of IGV settings on SNV variant page
  • Cases analyzed once shown as rerun
  • Missing case track on case re-upload
  • Fixed severity rank for SO term "regulatory region ablation"

Changed

  • Refactor according to CodeFactor - mostly reuse of duplicated code
  • Phenomodels language adjustment
  • Open variants in a new window (from variants page)
  • Open overlapping and compound variants in a new window (from variant page)
  • gnomAD link points to gnomAD v.3 (build GRCh38) for mitochondrial variants.
  • Display only number of affected genes for dismissed SVs in general report
  • Chromosome build check when populating the variants filter chromosome selection
  • Display mitochondrial and rare diseases coverage report in cases with missing 'rare' track
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