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Release Notes for Variation Viewer 2.1.4 (July 25, 2019)

New Features and Improvements

  • Updated to Generic Browser Components v.2.7.0

Release Notes for Variation Viewer 1.5.6 (July 17, 2017)

Bug Fixes

  • Fixed Variant Table "Location" link opening the entire chromosome instead of zooming in to particular coordinates

Release Notes for Variation Viewe r 1.5.5 (April 26, 2017)

Bug Fixes

  • Fixed Variant Table incorrectly reporting no variants on non-chromosomal top-level sequences
  • Fixed unexpected scroll bar in Variant Table dialogs

New Features and Improvements

  • Updated to Generic Browser Components v2.3

Release Notes for Variation Viewer 1.5.4 (February 13, 2017)

Bug Fixes

  • Fixed missing toggle arrow icons in Variant Table

New Features and Improvements

Release Notes for Variation Viewer 1.5.3 (November 14, 2016)

New Features and Improvements

  • Updated to include September 2016 data from dbVar, ClinSNP

Release Notes for Variation Viewer 1.5.2 (September 12, 2016)

Bug Fixes

  • Fixed handling of percent-encoded values in the " filters " URL parameter

Release Notes for Variation Viewer 1.5.1 (August 29, 2016)

New Features and Improvements

  • Updated default genomic context to GRCh38.p7 ( GCF_000001405.33 ) and Annotation Release 108
  • Replaced all protocol-absolute HTTP URLs linking to Federal government domains with HTTPS or domain-relative equivalents
  • Updated Generic Browser Components (GBC) backend from v1.9 to v2.1

Bug Fixes

  • GBC 2.1 update includes minor bug fixes

Release Notes for Variation Viewer 1.5 (January 27, 2016)

New Features and Improvements

Bug Fixes

  • Fixed missing ClinVar "Highest review status" for many dbSNP alleles in inner row of Variant Table

Release Notes for Variation Viewer 1.4.1 (October 20, 2015)

New Features and Improvements

  • Further optimized performance of Variant Filters and Variant Table. Filter latency improvements:
    • Default initialization: 73% (2.2 s) faster. Average: 1 second.
    • Gene-level filtering: 71% - 74% (2.1 s - 2.4 s) faster. Average: 1 second.
    • Chromosome-level filtering: 62% - 68% (3.0 s - 8.8 s) faster. Average: 4 seconds.

Bug Fixes

  • Fixed unexpected track reordering upon reloading the page or switching assemblies
  • Fixed occasional flash (double loading) of Sequence Viewer when switching assembly if user-uploaded tracks are present
  • Fixed long file names overflowing beyond the status bar in "Your Data" widget
  • Fixed missing 'Reset all' wait icon in Firefox
  • Fixed occasional flash (double loading) of Variant Table when loading page with q URL parameter.
  • Fixed hanging filter count updates when same exact range is searched twice in immediate succession

Release Notes for Variation Viewer 1.4 (September 29, 2015)

New Features and Improvements

  • Added track sets and track collections
  • Added " Toggle all " arrow button to Variant Table header. See allele-level data for all variants in current page with one click.
  • Added validation of filters URL parameter , and user-friendly handling of invalid values .
  • Added toggling of filter-list display
  • Added link to NCBI Remap in "Pick Assembly" widget upon switching to GRCh37.p13
  • Improved documentation readability
  • Optimized performance of Variant Filters and Variant Table. Filter latency improvements:
    • Default initialization: 38% (1.8 s) faster
    • Gene-level interactions -- filtering, exon selection, loading new gene: 16% - 33% (0.6 s - 1.4 s) faster
    • Chromosome-level interactions -- filtering, loading entire chromosome: 28% - 42% (3.3 s - 6.3 s) faster

Bug Fixes

  • Fixed occasional overflowing value in optional "Alleles" column in Variant Table
  • Fixed indefinite hanging in Variant Table filter counts when panning or zooming to region with no variants matching user's filter selection from previous view
  • Removed unnecessary alert raised for when page is loaded with deprecated minor version of current major assembly in " assm " URL parameter
  • Fixed minor styling and layout issues

Release Notes for Variation Viewer 1.3 data update (August 6, 2015)

  • Backend data was updated to show dbSNP b144 data set.

Release Notes for Variation Viewer 1.3 (May 21, 2015)

New Features and Improvements

  • Searches like "4:10000000" or "X:30000000-35000000" are now treated as location searches, equivalent to "chr4:10000000" or "chrX:30000000-35000000". The "chr" prefix for chromosome names can be omitted in location searches.
  • Search now supports GenBank sequence identifiers like CM000667.2 and HSCHR6_MHC_APD_CTG1. These can also be combined with more specific genomic coordinates, e.g. CM000667.2:1000000-1500000.
  • The first search result is now automatically selected if its name matches the searched term. For example, searching "APOE" or "rs334" seamlessly loads APOE or rs334 into view, without users needing to manually select the first row.
  • NM-based HGVS expressions are now supported in the in q URL parameter , e.g. https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/variation/view/?q=NM_000237.2:c.106G>A
  • Improved usability in the Your Data widget and the handling of tracks when switching assemblies in the Pick Assembly widget.

Bug Fixes

  • Fixed minor styling issues.

Release Notes for Variation Viewer 1.2 update (December 4, 2014)

  • Backend data updated to show dbSNP b142 data set.

Release Notes for Variation Viewer 1.2 (October 2, 2014)

New Features and Improvements

  • Tab-separated values (TSV) format download.
  • Click on 'Edit columns' in variation table to add or remove columns.
  • New overview page .

Bug Fixes

  • The inner Variant Table for rs6025 omits several medical conditions associated with the T allele.
  • Changed the inner Variant Table field labeled 'Description' to 'Condition'.
  • Molecular functional consequence for some rs (ie. rs6025 reported 'synonymous variant' instead of 'missense variant' ) .

Release Notes for Variation Viewer 1.1.3 (May 13, 2014)

Versions 1.1.1 and 1.1.2 were for internal use only.

New Features and Improvements

  • Data updated to GRCh38
  • Support multiple assemblies (GRCh37.p13 and GRCh38)
  • Search using assembly component accession (ie. AL731561) for overlapping genes

Bug Fixes

  • Data loading error for table view
  • Return alt loci positions for search by RS

Release Notes for Variation Viewer 1.1 (April 22, 2014)

New Features and Improvements

  • Search by phenotype (via Entrez Gene)
  • Download XML report
  • Support result filter URL parameters
  • Minor UI updates
  • Faster sequence viewer loading

Bug Fixes

  • Slow sequence viewer loading

Release Notes for Variation Viewer 1.0 (January 7, 2014)

New Features

  • Initial Beta Version
  • ID search (Gene, dbSNP, and dbVar)
  • Gene selector
  • Exon navigator
  • Search Filter
  • User data upload
  • Custom linking with URL parameters