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MIP 7 compatibility and bugfixes

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@northwestwitch northwestwitch released this 13 Sep 09:24
v.4.7.0
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Learn about vigilant mode.

New Scout release 4.7.0

Added

  • Export genes and gene panels in build GRCh38
  • Search for cases with variants pinned or marked causative in a given gene.
  • Search for cases phenotypically similar to a case also from WUI.
  • Case variant searches can be limited to similar cases, matching HPO-terms,
    phenogroups and cohorts.
  • De-archive reruns and flag them as 'inactive' if archived
  • Sort cases by analysis_date, track or status
  • Display cases in the following order: prioritized, active, inactive, archived, solved
  • Assign case to user when user activates it or asks for rerun
  • Case becomes inactive when it has no assignees
  • Fetch refseq version from entrez and use it in clinvar form
  • Load and export of exons for all genes, independent on refseq
  • Documentation for loading/updating exons
  • Showing SV variant annotations: SV cgh frequencies, gnomad-SV, local SV frequencies
  • Showing transcripts mapping score in segmental duplications
  • Handle requests to Ensembl Rest API
  • Handle requests to Ensembl Rest Biomart
  • STR variants view now displays GT and IGV link.
  • Description field for gene panels
  • Export exons in build 37 and 38 using the command line

Fixed

  • Fixes of and induced by build tests
  • Fixed bug affecting variant observations in other cases
  • Fixed a bug that showed wrong gene coverage in general panel PDF export
  • MT report only shows variants occurring in the specific individual of the excel sheet
  • Disable SSL certifcate verification in requests to chanjo
  • Updates how intervaltree and pymongo is used to void deprecated functions
  • Increased size of IGV sample tracks
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