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Single end BNDs, Methylation outliers, Phenomodel on case, Gens v4 links

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@dnil dnil released this 07 Apr 13:55
· 103 commits to main since this release
v4.109.0
a3371d8
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Learn about vigilant mode.

[4.109]

Added

  • Add a --type to the export case CLI, to limit the exported case search by analysis type (#6089)
  • MANE Transcripts as a default IGV track for alignments in genome build 38 (#6127)
  • Accept single end BNDs (#6132)
  • Update analysis type for case's individual/sample using scout update individual command (#6142)
  • Filter methbat outliers by significance ("HypoMethylated", "HyperMethylated", "HypoASM", "HyperASM") (#6140)
  • --force flag to force load research variants hitting a certain gene/region into a clinical case (#6153)
  • Download as PDF button on ACMG sandbox page (#6152)
  • Links to gDNA IGV view from variantS page also for WTS outliers (#6151)
  • Pick phenotype terms (HPO, OMIM, ORPHA) to be assigned to a case from a phenomodel object (#6138)
  • Methylation outliers population frequency filter and clinical filter (#6156)

Changed

  • Export genotype with gene variantS search (#6088)
  • igv.js version to 3.8.0 - fixes e.tags error popup issue (#6096, #6118)
  • Rework rank model file loading, allowing full URI (#6090)
  • Refactored scout delete commands and relative tests into separate modules (#6102)
  • The gens extension now generates version appropriate links (#6105)
  • Refactored snv and cancer snv variants code to share same routines as other variant categories (#6116 and #6128)
  • On managed variants page, print maintainers names instead of emails/ids (#6121)
  • Enable ClinVar test API URL by default on Scout demo config settings (#6129)
  • ClinVar settings (API and list of users allowed to send API submissions) are no longer shown only to admin users (#6134)
  • Refactor load research CLI to raise a FileNotFoundError with aggregated missing configured research files per case (#6148)
  • Make gene panel's display name editable by users, if they are panel maintainers or admins (#6147)
  • Rank model URLs can now be filenames, if not starting with "http" (#6150)
  • Methbat outliers significance filtering extended with "AlleleSpecificMethylation" and "imprint" (#6156)
  • Custom IGV tracks settings shown on variant don't depend on the specific variant genome build (#6165)

Fixed

  • Comments' text wrapping in ACMG classifications exported as PDF (#6086)
  • Individual breakpoint gDNA IGV links should not trigger split locus view (#6103)
  • Introduced a submittedAssembly field on Oncogenicity ClinVar submissions documents containing variants described by HGVS (#6113)
  • Main dropdown menu (#6120)
  • MT chromosome is hard to reach in Firefox dropdown selectpicker (#6123)
  • Parse also OMIM Digenic dominant (#6157)
  • Visibility of footer buttons on ACMG classifications documents exported to PDF (#6166)
  • Typo in compounds check when applying saved custom filters (#6170)
  • Use liftOver with omics variant build coordinate also for gDNA variants (#6168)
  • Gens case button on structural variant page with region and variant (#6176)
  • Allow download of local rank model files as custom reports (#6174)

Full Changelog: v4.108.2...v4.109.0

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