You can subscribe to the VaRank Announcement Mailing List if you want to be notified by email whenever a new release of VaRank becomes available.
To subscribe, send an email to veronique.geoffroy@inserm.fr with the subject line "VaRank SUBSCRIBE". Please, give your full name, your institution/organization and your country in the body (This is optional). You'll get an email back right away confirming that you've been subscribed to the VaRank Announcement Mailing List. To unsubscribe, send an email to veronique.geoffroy@inserm.fr with the subject line "VaRank UNSUBSCRIBE". You'll receive an email confirming that you've been unsubscribed from the VaRank Announcement Mailing List.
The list is for announcements only -- you cannot post to it.
VaRank News
Jun 04, 2021: VaRank version 2.0 is posted
- refactor: Use of a SQLite database to improve the running time
Apr 29, 2021: VaRank version 1.5.2 is posted
- feat: Add the genome build in the outputfile names
Apr 26, 2021: VaRank version 1.5.1 is posted.
- feat: The phenotype-driven analysis is now done by using the configfile
- doc: Update of the Tests directory.
- refactor: Refactoring the code for the writing of unnanotated variants
- feat: Display the hostname information
- feat: Add bugfix for MES processing
Feb 02, 2021: VaRank version 1.5 is posted.
- Include phenotype-driven annotations based on Exomiser (Smedley et al., 2015) and HPO (Kohler et al., 2019)
>> The "hpo" option can be used jointly with the "SamOut" option. This allows annotations to be added to samples sharing the same phenotype
>> The download of Exomiser annotations is automatic (not distributed with the sources)
- For a variant annotated on several transcripts from a same gene, only a single transcript from all transcripts available for this gene is reported in the following order of preference:
>> The transcript with the best VaRank score
>> The transcript with the longest CDS
>> The transcript with the longest transcript
- Add 22 novel gene-based annotations (ACMG gene list, HI, pLI, LOEUF, OMIM...) in the ExtAnn directory (detailed in the "Annotation columns available in the output files" section in the README.
- Add bugfix for handling lines with only a tabulation and no data in the configfile
- Improve the path displayed for the uniprot and refseq options
- Removing of HGMD columns annotations (due to the termination of HGMD annotation with the Alamut Batch version 1.10)
Aug 30, 2018: VaRank version 1.4.3 is posted.
Fixed Issues/changes:
- VaRank installation directory contains an ExtAnn directory that is now used by default to list all the additional files provided there
- Several new annotations have been added (gene intolerance to a loss of function variation, haploinsufficiency...)
- Only the first annotated gene of each variant will be annotated with external annotations
- For a variant annotated on several transcripts of a same gene, keep (i) the transcript annotation with the best score or (ii) with an equal score the longest transcript annotation
Jun 5, 2018: VaRank version 1.4.2 is posted.
Fixed Issues/changes:
- Add bugfix concerning Alamut annotation
Jun 1, 2018: VaRank version 1.4.1 is posted.
Fixed Issues/changes:
- Add bugfix concerning NNS annotation with Alamut (previous Alamut annotations need to be removed before to run a VaRank analysis again)
Apr 17, 2018: VaRank version 1.4 is posted.
Fixed Issues/changes:
- In order to add more flexibility to the output files, the user can now select the annotation columns and their order using the configfile
- Warning: several output column names have changed. Please check in the README file
- Several new annotations have been added (gnomAD, Align GVGD, gene inheritance mode...)
- Due to a high false positive calls observed for indels in the EVS dataset, the EVS annotations have been removed from the output and automatic filtering
- Support Alamut-batch version 1.6 to 1.9 (January 2018)
- Support SnpEff version 4.2 to 4.3 (build 2017-11-24) (Requires Java 1.8)
- Add bugfix: in some cases, a variation could be annotated using the non optimal isoform or gene (i.e. a variation localized either downstream of gene1 or in an intron of gene2 is now annotated preferentially to the intron of gene2)
- Variation with a depth of coverage equal to 0 are now annotated and reported in the output files
- Add bugfix: a variation associated with 2 genes and annotated with a pathogenic effect from ClinVar can not lead to the report of the non optimal gene anymore
Aug 04, 2016: VaRank version 1.3.5 is posted.
Fixed issues/changes:
- Support version 1.5.2 (July 2016) of Alamut-batch including novel local splice effect scores and branch point analysis
- Variants causing a premature stop codon in the coding sequence are now reported as "stop gain" in the codingEffect output field instead of "nonsense" which is now deprecated
- Change in ExAC annotations: homozygous frequencies are now replaced by the homozygous count
- Add of the --outputDataVersions when running Alamut-batch (reporting of databases names and corresponding versions)
- Add of the "-vcfFields" option. Allows to selectively report fields from the INFO column to the output files.
- Add of the "-SamOut" option. Write output files only for selected samples (not for all samples of all VCF input files).
- Enhance Alamut Batch error messages
- Add bugfix concerning external annotations (when containing "{}" characters)
- Add bugfix concerning detection of the number of read for the variant from the vcf file (with NR, AD, AC, AO and DV fields)
Mar 01, 2016: VaRank version 1.3.4 is posted.
- Add bugfix concerning scoring variations in ClinVar with "conflicting status"
Jan 18, 2016: VaRank version 1.3.3 is posted.
- Add bugfix concerning the vcfdir names containing "vcf"
Dec 18, 2015: VaRank version 1.3.2 is posted.
- Add bugfix for the specific treatment of allele count to compensate bad behavior from Torrent Suite VCF files
Dec 15, 2015: VaRank version 1.3.1 is posted.
- Add of the "AlamutProcesses" option (available only with the "standalone" Alamut version)
- Add of the "AlamutAlltrans" option (available only with the Alamut Batch annotation)
- Add bugfix concerning scoring of the "stop loss" and "start loss" variants.
Nov 20, 2015: VaRank version 1.3 is posted.
- Compatibility with the version 4.2 of the VCF format. Reporting in the VaRank outputs of the "*" alleles (upstream deletion)
- Scoring scheme improvement: new category for splice site creation and score adjustment for some categories (available only with Alamut Batch annotation)
- Creation of a new output file (VaRankIDlinkedToVCF.txt), giving for each VaRankID a correspondence between the genome position and the VCF positions (can be different for indels)
- Add of the "SpSiAnnotation" column
- Add of the "-SamVa" option. A new column (SamVa) available to display samples and zigosity status different from the reference sequence within the barcode (up to 10 different samples)
- Add bugfix concerning scoring of the dbSNP pathogenic variants
- Add bugfix for some rare situation in the VCF in which the multiple alternate variants would be skipped and not counted in the barcode
- New method to filter out benign annotated variants in dbSNP
- Compatible with Alamut Batch 1.4.2 (Jul. 2015)
- Compatible with SnpEff V4.1 L (2015-10-03)
- Update of the statistics treatment
- Add bugfix for SnpEff annotations
Jul 24, 2015: VaRank version 1.2.5 is posted.
- Add bugfix concerning interpretation of some specific VCF positions
Jun 16, 2015: VaRank version 1.2.4 is posted.
- Rename "DB" option in "pph2DB". "pph2DB" option can now be correctly set by user.
- Change mode of PPH2 lock files (avoid bug in case of different users)"
- Add bugfix concerning shift in the number of columns when a local installation of PPH2 is used
- Add bugfix concerning metrics on allele frequency
- Add bugfix concerning treatment of the external annotations (with some specific extann files)
Fev 26, 2015: VaRank version 1.2.3 is posted.
- Support version 1.4.0 (Fev. 2015) of Alamut-batch (adds annotations from ClinVar and ExAC)
- Support version 4.1b of SnpEff
- Addition of the "Allele frequency" annotation (allele frequency in all samples analyzed together)
- Addition of ExAC annotations and filtering with the Alamut-batch annotation engine
- Addition of ClinVar annotations with the Alamut-batch annotation engine
- Modification in the use of the dbSNP MAF for filtering
- Add bugfix concerning interpretation of some specific VCF positions
Fev 02, 2015: VaRank version 1.2.2 is posted.
- Speed improvment of SnpEff annotation
- Adds bugfix concerning SnpEff annotation
- New treatment of the external annotations (in case of one variant that could be attributed to several genes, all genes are annotated)
Jan 30, 2015: Creation of the VaRank Announcement Mailing List
- There now is a VaRank Announcement Mailing List that you can subscribe to if you want to be notified by email whenever a new release of VaRank becomes available.
Jan 27, 2015: VaRank version 1.2.1 is posted.
- Adds bugfix concerning SnpEff annotation
Jan 20, 2015: VaRank version 1.2 is posted.
- New annotation engine: support of SnpEff in addition to Alamut-batch.
- Addition of 1000g annotations and filtering
- Scoring scheme fully configurable by the user
- Tutorial V1.0
Nov 28, 2014: VaRank version 1.1.1 is posted.
- Extended support of gzip files to the external annotation input file.
- Default adjustment score set to 5 (before was 10) for the PolyPhen-2 and SIFT prediction.
The score can now also be modified by the user (with B_phastCons, B_SIFT and B_PPH2 options)
- Addition of error messages to improve support (incorrect input file, Alamut not accepted Alamut-batch License, not supported version of Alamut-batch, ...)
- Adds a bugfix concerning pph2 analyses
Nov 25, 2014: New VaRank web site configuration.
Nov 7, 2014: VaRank version 1.1 is posted.
- Supports version 1.3.0 (Oct. 2014) of Alamut-batch (using new clinical significance terms from ClinVar)
- Supports gzip VCF files in input
- Offers 3 new annotations columns in the output files:
- Avg_TotalDepth: Total read depth average at the variant position for all samples analyzed that have the variation
- SD_TotalDepth: Standard deviation associated with Avg_TotalDepth
- Count_TotalDepth: Number of samples considered for the average total read depth
- Adds a minor bugfix concerning pph2 analyses
- Updated VariantID nomenclature for large indels
