Changelog

v 1.13.6 (16.08.2024)
General changes:
  • Improved API security
  • Added variant upload and variant check through api
Bugfixes:
  • Fixed a visual bug when the request to start a new upload to HerediCaRe task was erroneous, but the ClinVar upload was successful
v 1.13.5 (15.08.2024)
Bugfixes:
  • When using a non-default redis port background tasks would not work correctly. This was resolved.
  • Fixed a bug when uploading variants to HerediCaRe that are unknown by HerediCaRe
v 1.13.4 (25.07.2024)
General changes:
  • Added full import of HerediCaRe VIDs button to admin dashboard alongside the preexisting incremental update
  • Updated HerediClassify to v1.0.4
  • Improved admin dashboard variant import summary page. It now loads way faster
Bugfixes:
  • Fixed a rare bug where HerediCaRe VIDs were inconsistently annotated
  • pm2_pp + 1x pvs now correctly classifies as likely benign in ATM v1.3.0 scheme
  • Fixed a bug that the annotation would fail when the consequence annotation tool would not get any consequences from ensembl
  • Very large variants would fail to recieve literature from litvar2 which would result in an erroneous annotation
v 1.13.3 (23.07.2024)
Bugfixes:
  • Searching for specific variants would not apply filters correctly
v 1.13.2 (22.07.2024)
General changes:
  • Added retry import button for single failed HerediCaRe VIDs
  • Improved HerediCaRe VID information page
  • Added more fine grained variant type search: added insertion, deletion and delins. Small variants are now single nucleotide variants.
Bugfixes:
  • Fixed a bug that CrossMap could not be invoked when lifting between genome versions
  • Variant annotation would fail when the HerediCaRe API returned a bad status code
  • Fixed a bug where variants could not be hidden
v 1.13.1 (18.07.2024)
General changes:
  • Updated ClinVar to version 2024-07-16
  • Updated HerediClassify to version 1.0.3
  • Improved security for flashed messages
  • Added HerediVar link to variant banner on multiple pages
Bugfixes:
  • Fixed a bug where users were unable to add variants to lists from public editable databases created by another user
v 1.13 (05.07.2024)
General changes:
  • Publish and insert queue history pages are now paginated for better scalability
  • Improved single HerediCaRe VID import
  • Updated PFAM protein domain external links to link to InterPro
  • Increased login idle timer
  • Now the REVEL score of the best transcript is shown first
  • Enabled HerediCaRe uploads
Bugfixes:
  • Resolved an issue where the consensus classification needs upload warning sign was shown on requested publish status
  • The ClinVar and HerediCaRe status showed status requesting when any variant was uploaded to heredicare/clinvar
  • The ClinVar and HerediCaRe status pills did not show the error message in specific cases
  • Fixed a bug that caused dynamically generated VCFs to not show the download diaglogue
  • Removed wrong chromosome from check variants page
  • Classification criteria were not wrapping properly on the variant history page
  • In specific cases the cancerhotspots annotations were incorrect
  • Fixed an issue when two criteria had the same mutually exclusive criterion target and both were selected. If the use would unselect one of them the mutually exclusive criterion would be enabled for selection even though it shouldn't
  • When a variant was not annotated or did not have any consequences the "no scheme" would be preselected on the variant classify page. Now, the correct selected default classification scheme is selected
  • Fixed an issue where the previous status of ClinVar and HerediCaRe uploads would be shown on the variant display page upon status updates
  • Fixed a bug where sometimes wrong COSMIC links would be generated
v 1.12 (17.06.2024)
General changes:
  • Added updated classification schemes:
    • PALB2: v1.0.0 -> v1.1.0
    • ATM: v1.1.0 -> v1.3.0
    • BRCA1: v1.0.0 -> v1.1.0
    • BRCA2: v1.0.0 -> v1.1.0
  • Previously, moderate benign criteria were colored in pink. Now, very strong benign criteria are shown in this color.
  • Removed extra download for structural variants. Instead they are now combined in one file with small variants. Also, IGV now shows one track for all classified variants.
  • Improved session security
  • Added an API endpoint for access of consensus classifications programmatically
  • Added API documentation
Bugfixes:
  • Selecting pm2_sup in ATM gene specific scheme or bp1_str in BRCA1/2 schemes caused wrong calculated class when selecting another supporting or strong criterium.
  • The force download url for erroneous vcfs was broken
  • Fixed a bug where the header line for annotated literature was incorrectly called 'pubmed' instead of 'literature'
v 1.11 (31.05.2024)
General changes:
  • Update downloads page. Added full data download and database versioning. A new HerediVar full VCF version is calculated every month.
  • Added download archive for previous full VCF downloads
  • Added HerediCaRe upload and improved CliVar upload:
    • Single variants from variant details page
    • Multiple variants from user variant lists page
    • All variants which recieved an update since the last upload from the admin dashboard
  • Updated gene specific PTEN ACMG scheme to v3.1.0
  • The consequences in downloaded vcf files and the variant details page does not contain the pfam protein domain anymore. Instead it was moved to a transcript specific variant annotation field (pfam_domains= in vcf downloads).
  • Moved consequence calculation from VEP to VcfAnnotateConsequence tool from the ngs-bits library GitHub. VcfAnnotateConsequence improves the quality of consequences.
  • Improved the comment that is uploaded to external databases. It now also includes unselected criteria and selected literature.
  • 4M classifications are now uploaded to ClinVar without scheme. Reason: 4M classification is not specified in ACMG spec.
  • Enabled consensus classifications without scheme and their upload to ClinVar.
  • Implemented variant upload to HerediCaRe.
  • Increased security by hardening Keycloak Database and removing popovers with enabled HTML content
  • Added class R (established risk allele) for selection in classifications without scheme
Bugfixes:
  • The variant type search would only show small variants even though both, small and structural variants are selected after querying the second search within a user defined list. This issue was resolved.
  • Previously, the variant search would result in an error when searching for genomic ranges and ticking at least one variant type.
  • Improved genomic range search and its documentation
  • The variant list search was not working properly. This issue was resolved.
  • When a variant did not have an annotation, fetching the annotation status would result in an error.
  • Fixed a bug where the assay quantification was inserted to HerediClassify as a percentage instead of a decimal number.
  • Fixed a bug that caused a variant to not be found when the 'chr' prefix was omitted in the variant string search
  • Fixed a bug that caused variants with multiple genes to not automatically select the best classification scheme
  • Criterium PM5 was previously only moderate strength although the specifications suggest only supporting strength for this criterium in ATM gene specific ACMG scheme. This issue was resolved.
v 1.10.2 (15.04.2024)
Bugfixes:
  • When selecting two or more very strong criteria the resulting class was 3 previously. Now it is 5. Similar with stand-alone criteria.
  • The color of classified variants which only have a consensus classification in HerediCaRe of 3+ or 3- were previously shown in black in IGV. This is fixed now and they are shown with their proper color.
  • Fixed some wording.
v 1.10.1 (12.04.2024)
Bugfixes:
  • Removed empty tab from small variant upload
v 1.10 (12.04.2024)
General changes:
  • When too many variants were added to a user defined variant list the request would previously time out. This has been resolved by adding the variants to the list in the background. A status pill is now shown when the user wants to view a variant list where variants were added from the browse variants table.
  • Updated documentation
  • Activated automatic classification algorithm
  • Added tooltip to criterion select on classify page to explain what the different states mean
  • Added CDH1 ACMG classification scheme
Bugfixes:
  • Fixed a bug where the cancerhotspot annotations would be erroneous: If variants map to the same position in grch38 or are equal when left normalized their cancerhotspots annotations are now summed up
  • Fixed a bug that caused criteria buttons to be unchecked when mutually exclusive criteria were unselected
  • If a variant had multiple HerediCaRe VIDs it would not show the warning in the n_fam and n_pat annotations that the counts might be inaccurate
v 1.9 (12.03.2024)
General changes:
  • Added comments from HerediCaRe center specific classifications
  • Added gnomAD non-cancer scores & faf95 popmax value
Bugfixes:
  • Fixed a bug where the HerediCaRe center specific classifications were not shown when the HerediCaRe consensus classification was unavailable
  • When there were multiple rows in the HerediCaRe classifications table the center details button would always open and close details of all rows
  • Previously, an empty HerediCaRe table was shown on the variant details page when the variant was known to HerediCaRe, but was not classified. The empty table was removed in this case
  • Longer insertions were previously clogging the header line. This was fixed by cropping the reference and alternative bases if their length is large
  • Fixed a bug where vcfs were not downloadable when the variant had HerediCaRe annotations but no center specific classifications
v 1.8.2 (26.02.2024)
!! The automatic classification algorithm is currently under construction. HerediVar is already prepared for it. Thus, you might encounter disabled buttons or dummy data. It will be enabled in a future update
!! Scores from likelihood ratio tests are currently under construction. A simple reannotation is required to show them on HerediVar once they are ready to be downloaded from HerediCaRe.
Bugfixes:
  • Fixed a bug where the SpliceAI score was not shown correctly when it is "."
  • In rare cases the submission condition in ClinVar submissions is na with a description. This case is now handled properly and does not produce erroneous links.
  • Fixed a bug when the assay comment for splicing assays could not be inserted due to length
v 1.8.1 (23.02.2024)
General changes:
  • Changed is_selected for classifications to a more descriptive state information in downloaded vcf files
Bugfixes:
  • Fixed a bug when there were no HerediCaRe center classifications but a consensus classification from HerediCaRe
  • A selected criterium would automatically uncheck if a mutually exclusive criterium was unselected and the mutually exclusive criterium itself is mutually exclusive with the selected criterium
  • Fixed default strength for supporting criteria in ACMG standard scheme
  • Fixed wrapping of PVS1_mod criterium
  • Fixed a bug where the SpliceAI scores would not show on longer indels
v 1.8 (21.02.2024)
General changes:
  • Added scores from likelihood ratio tests.
  • Removed BayesDel annotations from TP53 DB, because they are annotated from a dedicated BayesDel anntation anyway.
  • Improved Cancerhotspots internal representation, display & representation in the INFO column of vcfs
  • Added HerediCaRe center specific classifications
  • Added CSpec BRCA1/2 assays to annotation algorithm
  • Copy evidence of user classifications to a consensus classification now also automatically selects the state correctly
Bugfixes:
  • Fixed a bug where some variants got raw SpliceAI scores instead of the masked ones
  • When constructing an URL for the variant details page it was previously not possible to omit the "chr" prefix for the chromosome
  • Task force protein domains are now shown correctly
  • Transcripts on the negative strand were shown as if they were on the positive strand in the IGV browser
  • Fixed a bug when the user clicked on logout even though the user was already logged out (for example because of inactivity)
  • The default scheme was not properly working. It would automatically select the last scheme in the list as default no matter what was selected on the admin dashboard
  • Fixed a bug when updating ClinVar submissions
  • When selecting any BP criterium the enigma BRCA1/2 schemes would instantly switch to class 2. This is now fixed and only BP1_str triggers class 2
  • Previously the class by scheme was not updated correctly when the user updated their classification
  • Fixed a bug in the criteria column of the automatic classification results that would shrink to width zero when the screen is resized
  • Fixed a bug where unselected criteria where shown as selected for consensus classifications

Changelog

v 1.7 (16.01.2024)
General changes:
  • Added form to create structural variants: DEL, DUP, INV
  • Added structural variants to browse variants table
  • Added START, END, SVTYPE, IMPRECISE info columns to vcf with structural variants
  • Added the general comment to the classified variants download
  • Added a separate download link for all classified structural variants
  • Added structural variants track to IGV
  • Added the coldspot annotation
  • Added variant search which allows the user to search directly for a specific variant using this format: chrom-pos-ref-alt OR chrom-start-end-sv_type in case of structural variants
  • Changed External ID search to overall ID search. It now also allows to search for heredivar variant ids.
  • Update search help
  • Added variant type search option
  • Updated ClinVar to v. 20240207
Bugfixes:
  • Fixed tooltips in browse variant table
  • The annotation service would fail when the variant does not have a dbsnp rsid
  • Fixed a bug that increased the size of the consensus classification label for class 4M
  • The clinvar variation was in the downloaded vcf files twice. Removed one of the copies. The clinvar variation id info is now called "clinvar"
  • In rare cases ClinVar submissions are missing which would result in an error when downloading the vcf file. In such cases the clinvar_submissions info in the downloaded vcf file will be set to None
  • Fixed a bug that prevented the user to change the state of criteria when using microsoft edge
Known issues:
  • HerediCare Center specific classifications are not available
  • HerediCare priors, log likelihood, segregation & cooccurance are not available
v 1.6.1 (11.01.2024)
Bugfixes:
  • Searching for 4M criterium with include_heredicare option would result in an error
  • Searching for class 4 consensus classification with include_heredicare option previously resulted in consensus class 4 and heredicare class 3+
v 1.6 (10.01.2024)
General changes:
  • Classifications can now be submitted without selecting any criterium
  • Added the ClinGen gene specific ACMG classification scheme for ATM
  • Added page to hide classification schemes:
    • disable schemes
    • set default scheme
  • Improved automatic selection of schemes based on genes
  • Changed suffixes from criteria with differing strenghts
  • Download of all classified variants now also contains all variants which were only consensus classified in heredicare. Also added a source of the classification info column
  • Added gnomAD v4 link to variant banner
  • Variant annotations can now be aborted from the admin dashboard
  • Added a button to reannotate all aborted variants from the admin dashboard and moved the reannotate erroneous variants button to the (Re-)annotate tab of the admin dashboard
  • Added automatic classification algorithm v1.0
  • Added the automatic classification result to the browse variant table & variant details page
  • Added automatic classification search
  • Added a button to the admin dashboard to annotate all variants which are missing an annotation
  • Updated VEP from 107.0 to version 110.1
  • Added possibility to "unselect" a criterium when there is evidence that this criterium does not hold
  • Added button to automatically select criteria based on the automatic classification algorithm
  • Added automatic classification algorithm results to vcf export
  • Added flag to vcf export of heredivar classifications if a criterium was selected or not selected in response of evidence
  • Added all external ids to variant vcf export including for example heredicare VIDs, rsids, cosmic ids, etc.
  • Improved display of intergenic variants on variant details page
  • Changed wording in contact form & enabled contact form
Bugfixes:
  • Fixed a bug where the criterium strength addition to the label would reset when the default strength was not its original strength.
  • Fixed the order of selectable criteria strengths on the classify variants page
  • Fixed a bug when submitting 4M classifications
  • Previously, updates to ClinVar submissions were not working & removed the 'customAssertionScore' from ClinVar submissions
  • Fixed a bug when trying to add all variants from a search to a list
  • In BRCA2 v1.0.0 criteria supporting strength was not selectable
  • Sometimes, the classification scheme was not changeable in consensus classifications
v 1.5 (17.11.2023)
General changes:
  • Added option to include heredicare consensus classififcations in consensus classification search
  • Added BayesDEL annotation
  • Improved ClinVar review status & summary display
  • Improved range search. Each range search entry must now be of the format: chrom<sep>start<sep>end. With <sep> being either :, -, space or tabulator. The chromosome number can start with 'chr', but you can also choose to omit it.
  • Added external id search. Which allows to search for external ids like heredicare VIDs, COSMIC COSV ids or dbSNP RSIDs.
  • Added cDNA search
  • Update search help
  • Added COSMIC COSV ids & moved COSMIC links from consequence table to the variant banner.
  • Added GnomAD popmax allele count (AC) annotation
  • Updated documentation
  • Added annotation search
  • The classification comment is now optional
  • REVEL annotations are now transcript specific and show the maximal value in the overview. The details list REVEL scores for all annotations
  • Additional warnings added to annotation service
  • User classifications can now be deleted by the user that created it
  • Renamed class 4 to 4M & changed its color to orange
  • Renamed PALB2 v1.0.0 & TP53 v1.4.0 classification schemes
  • Improved performance of transcript track in IGV
Bugfixes:
  • Fixed a bug where the "gene", "your classification" and "consensus classification" columns were not clickable in the browse variant table
  • Fixed a bug where in some cases some ClinVar submissions were not annotated
  • Fixed a bug which caused some annotations to be erroneous, when importing variants from HerediCare
  • Fixed status of deleted VIDs upon variant import
  • In some cases the consequence was duplicated in the variant banner.
  • Increased the size of the criteria display buttons, because the label did not fit into one line in some cases.
  • Fixed a bug when submitting incomplete information on the "submit to ClinVar" page
Known issues:
  • HerediCare Center specific classifications are not available
  • HerediCare priors, log likelihood, segregation & cooccurance are not available
v 1.4.1 (02.11.2023)
Bugfixes:
  • Fixed a bug where the user was unable to insert classifications by the new ClinGen criteria
v 1.4 (27.10.2023)
General changes:
  • Update landing page
  • Moved previous changelog announcements to a new page
  • The admin dashboard now allows reannotation of a user defined set of databases
  • The admin dashboard now shows an overview of all annotations and annotation errors / warnings
  • Added a contact form where unregistered people can ask a question about a variant
  • Added suffix to criteria names if the selected strength is not the default strength
  • Variants can now be hidden
  • The variant list can now be sorted by chromosomal position and insertion date
  • The page size in the variant list can now be adjusted
  • Consensus classifications are now preselected from the most recent consensus classification for each scheme
  • Added four new ClinGen ENIGMA schemes for specific genes: BRCA1 (v.1.0.0), BRCA2(v.1.0.0), TP53 (v.1.4.0), PALB2 (v.1.0.0)
  • Changed SpliceAI annotations to masked ones
  • Added variant import from HerediCare
  • Added HerediCare number of families and heredicare number of cases annotations
  • Improved criteria popover
  • Added variant import history page
  • Enabled HerediCare annotations in admin dashboard
  • Added downloads page
  • Added variant check page
Bugfixes:
  • Variants are now not selected by default on the search variants page
  • Abbreviations for criteria are now written with upper case letters
  • Disabled criteria were not shown correctly
  • Popovers now stay open when clicked and close when the user does not click inside the popover
  • Fixed a bug where the ClinVar annotation was erroneous which happened when there were missing submissions
  • Fixed a bug where the consequence annotation was erroneous which happened when the variant was large and spanned multiple exons / introns
  • Fixed a bug where the user was unable to download variants which are not annotated
  • Fixed a bug where the user could not search for class 3+
  • The date is now inserted correctly when classifying variants. Preexisting classifications did not change (this is fixed starting from 24.10.23).
Known issues:
  • COSMIC links do not work sometimes
v 1.3 (19.06.2023)
General changes:
  • Added checkboxes to variant table which allows more fine grained collection of variants in lists
  • Added information about the chosen criteria to the comment of a ClinVar submission from HerediVar
  • Updated documentation
  • The strength of all ACMG criteria can be adjusted now
  • Added continuous numbering of variants in variant lists
  • Added 3+ and 3- classes. They can be selected manually from the dropdown
  • Added important variant information to classify page
  • Mane select transcripts are now shown in green in IGV
Bugfixes:
  • Fixed ClinVar uploads
    Classifications are currently submitted to the ClinVar TEST ENDPOINT which is reset periodically! None of your ClinVar submissions will go live at the moment.
  • Fixed a bug when the user tried to access a non existing variant list
  • Improved performance of variant table
  • Fixed a bug where the user was unable to search for gene:hgvs strings in the variant table
  • Classified variants in IGV browser are now shown with the color scheme corresponding to the classification
  • Fixed a bug where some characters were replaced by the url encoding in HGVS strings
  • Fixed a couple of CSP errors
  • Fixed the colors of classified variants in IGV
  • Fixed colors of acmg criteria buttons
Known issues:
  • COSMIC links do not work sometimes
v 1.2 (12.05.2023)
General changes:
  • Improved user registration form
  • Added profile page which allows each user to edit their name, mail and affiliation by themselves
  • Added possibility to search for multiple lists simultaneously
  • Added duplicate, intersect, subtract and union actions for user variant lists
  • Updated documentation
Bugfixes:
  • Fixed a bug where the user was able to upload multi allelic variants
  • Fixed a bug where the user was able to insert invalid variant sequences
  • Navigation is now shown independent of scroll position on documentation page
  • Fixed a bug when searching it would not show any variants
v 1.1 (08.05.2023)
General changes:
  • External links now open a new tab on left click
  • Added documentation
Performance changes:
  • Added client-side pagination of the literature table
v 1.0
Initial release