April, 14, 2023: AnnotSV has been added to bioconda
- AnnotSV has been added to bioconda.
AnnotSV can also be installed via conda using this command: conda install -c bioconda annotsv
- A docker image is available here.
Pull this container with the following Podman command: podman pull quay.io/biocontainers/annotsv
Pull this container with the following Docker command: docker pull quay.io/biocontainers/annotsv
- A singularity image is available here.
April, 14, 2023: AnnotSV version 3.3.5 is posted
- Add documentation on the "-includeCI" option
- Add bugfix for variantconvert use in GRCh38 (when setting the REF in the VCF output file)
- Add bugfix during the install (depending on the environment)
April, 11, 2023: AnnotSV version 3.3.4 is posted
- Among the “po_P_*_*” features, redundancy is now removed ONLY from “po_P_*_phen” and “po_P_*_hpo”
=> AnnotSV keeps now the correspondence between “po_P_*_source”, “po_P_*_coord” and “po_P_*_percent” features
- Improvment of the running time (code part: SV partially overlapping with an established benign region)
- Update of the Makefile (variantconvert install)
- Remove requirement for ANNOTSV environment variable
- Add of the "INSTALL_code.sh" and "INSTALL_annotations.sh" bash files (for a basic manual installation)
- Add a check of the "#CHROM" header line
- Add of the "-variantconvertDir" option (path of the variantconvert directory). By default, the variantconvert tool distributed by annotSV is used
April, 11, 2023: Stay tuned for the latest news on AnnotSV developments
Given the success of the communication via github, the twitter account and the AnnotSV mailing list have been closed to favor a single channel.
- AnnotSV users can ask to be notified of AnnotSV activity ("AnnotSV Watchers").
- AnnotSV users can "star" the AnnotSV github, to make it easy to find the repository as they wish.
- AnnotSV users are free to create new issues on GitHub to suggest new annotations, features and reports.
March, 30, 2023: AnnotSV version 3.3.3 is posted
- Add bugfix for large input file
March, 28, 2023: AnnotSV version 3.3.2 is posted
- Add bugfix for SV partially overlapping with an established benign region. Ranking Impact
- Improve the 40 criteria (Loss) in the SV ranking
- Restrict the number of "po_B_*_someG_*" features to 20
March, 24, 2023: AnnotSV version 3.3.1 is posted
- Add bugfix with the use of the SVminSize option
- Report the minimal LOEUF value (among those of all overlapped genes) in the SV full length annotation
- Update of the variantconvert distribution (1.2.2 installed)
March, 23, 2023: AnnotSV version 3.3 is posted
- Add bugfix regarding genomic start coordinates. TSV and VCF output files are now both 1-based, with inclusive-end (whatever the input file format)
- Add interpretation of the square-bracketed SV breakend notations within the VCF.
This new module relies on the homogenization rules provided within the variant-extractor tool developed by Rodrigo Martín.
- Update of the variantconvert distribution (1.2.1 installed)
- Automation of the variantconvert module installaton
- Reformat of the unannotated.tsv file
- Add of the .gitignore file
- VCF format handling update. According to the VCF 4.4 specification, the SVTYPE has now been deprecated (due to redundancy with ALT).
The SV type is now extracted primarily from the ALT column, then from the SVTYPE field in the INFO column if available.
- Add bugfix for the TAD annotations update process
January 31, 2023: AnnotSV version 3.2.3 is posted
- "Samples_ID" field is now always reported in the output (default, sample = NA)
- Add the creation of a VCF output file from a "BED" SV input file. The "-vcf" and "-svtBEDcol" options are required.
- In VCF output, the GT is set to “1/.” for each SV if the GT is not given in input (BED input file)
- Add bugfix concerning Mouse annotation
January 06, 2023: AnnotSV version 3.2.2 is posted
- Add bugfix, update of variantconvert (configfiles: GRCh37/GRCh38, paths; headers) for the creation of VCF output
December 22, 2022: AnnotSV version 3.2.1 is posted
- Add bugfix concerning the partial overlap with some specific dbVar SV (same start and end locations)
December 20, 2022: Availability of vcf2circos
This is a standalone program which can generate Circos plot from an AnnotSV VCF output file.
The vcf2circos source code is downloadable under the GNU Affero General Public License v3.0 on GitHub.
December 13, 2022: AnnotSV version 3.2 is posted.
- Add of a new output format: VCF
- Add partial overlap annotation:
- Add 4 benign gain SV annotation: po_B_gain_allG_source, po_B_gain_allG_coord, po_B_gain_someG_source, po_B_gain_someG_coord
- Add 4 benign loss SV annotation: po_B_loss_allG_source, po_B_loss_allG_coord, po_B_loss_someG_source, po_B_loss_someG_coord
- Add 5 pathogenic gain SV annotation: po_P_gain_phen, po_P_gain_hpo, po_P_gain_source, po_P_gain_coord, po_P_gain_percent
- Add 5 pathogenic loss SV annotation: po_P_loss_phen, po_P_loss_hpo, po_P_loss_source, po_P_loss_coord, po_P_loss_percen
- Add the 2B, 2C, 2F, 2G and 4O criteria (Gain) in the SV ranking
- Update of the "make uninstall"
September 12, 2022: AnnotSV 3.1.3 is posted.
- Update Human annotations
- Use new ClinGen data source format ("OMIM ID" no longer reported)
- Removing of the DDG2P gene annotations (to avoid redundancy with GenCC)
September 09, 2022: Availability of variantconvert
This is a standalone program which can generate VCF output from an AnnotSV TSV output file.
The variantconvert source code is downloadable under the GNU Affero General Public License v3.0 on GitHub.
July 10, 2022: AnnotSV 3.1.2 is posted.
- Add important bugfix concerning the GRCh38 coordinates of the morbid genes
- Add bugfix concerning some Overlapped_CDS_percent values
- As part of the GenCC, the DDG2P gene annotations was removed from AnnotSV to avoid redundancy
November 25, 2021: AnnotSV 3.1.1 is posted.
- Add bugfix when setting the ANNOTSV global environmental variable with a final "/"
- Update the documentation, add of the AnnotSV logo
June 17, 2022: knotAnnotSV 1.1.2 is posted.
knotAnnotSV is now available under a new output format: a spreadsheet xlsm file that can be downloaded.
It is dedicated to large inputs and is compatible with thousands of SV, called from WGS, RNA-seq ...
It provides you with a customizable xlsm file (to display in a spreadsheet program), with expandable/foldable lines (full, split, annotations) to facilitate handling and interpretation.
November 08, 2021: AnnotSV 3.1 is posted.
- Change the -genomeBuild default value to "GRCh38" (instead of GRCh37)
- Use boolean values (instead of "yes"/"no") for the following option values: -candidateGenesFiltering, -includeCI, -overwrite, -reciprocal, -REreport, -REselect1 and -REselect2
- Add the Children’s Mercy Research Institute Benign SV annotations (n=502 WGS)
- Add the GenCC database for Gene-Disease relationship annotations
- Add CytoBand annotation
- Add novel regulatory element annotation:
- Add miRNA annotation (from miRTargetLink)
- Complete the RE_gene column output (the regulated gene name is detailed with more information: candidate gene annotation and data sources (RefSeq, ENSEMBL, EnhancerAtlas, GeneHancer and/or miRTargetLink))
- Add the "-REselect1" and "-REselect2" options to filter the RE_gene output
- Add the "-benignAF" option to change the allele frequency threshold used to select the benign SV in the data sources
- Add 4 annotation columns: B_gain_AFmax, B_loss_AFmax, B_ins_AFmax and B_inv_AFmax (maximum allele frequency of the reported benign genomic regions)
- Add new warnings if the compound heterozygosity analysis is not processed
- Add the "-version" option
- Take into account of a new format in the downloaded OMIM data (approved gene symbol)
- Add bugfix in case of leading or trailing white space in SV type values from the SV input BED file
- Add bugfix in case of no external BED annotation files used
- External BED annotation files can now also be used to report any feature overlapped with the SV (even with 1bp overlap)
- Add bugfix concerning the use of the "-candidateGenesFiltering" option
- Include "NA" in the "-rankFiltering" default option (default = "1-5,NA")
- Add bugfix concerning the use of the "split" annotationMode
- Add bugfix in the SV input BED file, last column could not have empty values. Replaced with "." if empty
- Add bugfix in section 5 of the SV ranking
- Set the ACMG_class to "NA" if not defined
- Update/Add Mouse annotations (CytoBand, miRNA from miRTargetLink)
May 22, 2021: The AnnotSV and knotAnnotSV web server has been published in NAR.
AnnotSV and knotAnnotSV: a web server for human structural variations annotations, ranking and analysis.
Geoffroy V, Guignard T, Kress A, Gaillard JB, Solli-Nowlan T, Schalk A, Gatinois V, Dollfus H, Scheidecker S, Muller J.
NAR. 2021 May 22. doi: 10.1093/nar/gkab402
December 19, 2020: AnnotSV 3.0 is alive!
- Major code rewrite and annotations sources reorganization
- Significant modification of the annotations column names
- Add 3 annotation columns: AnnotSV ranking score; ranking decision criteria; AnnotSV ranking class
- Pathogenic SV sources: dbVar, ClinGen, ClinVar, OMIM morbid genes
- Add 12 annotation columns:
P_gain_phen; P_gain_hpo; P_gain_source; P_gain_coord;
P_loss_phen; P_loss_hpo; P_loss_source; P_loss_coord;
P_ins_phen; P_ins_hpo; P_ins_source; P_ins_coord;
P_inv_phen; P_inv_hpo; P_inv_source; P_inv_coord
- Remove previous annotation columns from dbVar
- Benign SV sources: DGV, ClinVar, ClinGen, DDD, gnomAD, 1000g and IMH
- Add 8 annotation columns:
B_gain_source; B_gain_coord; B_loss_source; B_loss_coord;
B_ins_source; B_ins_coord; B_inv_source; B_inv_coord
- Remove previous annotation columns from DDD, DGV, gnomAD, 1000g and IMH
- Add new regulatory elements annotation (EnhancerAtlas)
- Merge regulatory elements annotations into a single column (RefSeq/ENSEMBL, EnhancerAtlas, GeneHancer)
- Update of the annotation data sources with the latest available versions
- The "overlap" option default is now set to 100 % in order to be compliant with the ACMG guidelines
- Add the percent of the CDS overlapped with the SV (in the "split" annotation lines)
- Add the number of overlapped genes in the "full" annotation lines
- By default, AnnotSV now expands the "start" and "end" SV positions with the VCF confidence intervals (CIPOS, CIEND) around the breakpoints (see the "includeCI" option)
October 13, 2020: AnnotSV version 2.5 is posted.
- Add of the "ENCODE blacklist", "Segmental Duplication" and "Gap" annotation datasets
- Fix a critical bug for DGV annotation (GRCh38)
- Add the distance / type to the nearest splice site after considering both breakpoints (distNearestSS and nearestSStype columns)
- Add the in-frame / out-of-frame information from overlapping genes (frameshift column)
- Add decision criteria explaining the ranking (previously available as a separate file)
- Remove of the ranking decision output file (*.ranking.tsv)
- Change the names of the values for the "tx" option:
- NM >> RefSeq
- ENST >> ENSEMBL
- Add bugfix allowing to use a configfile located in the same directory as the input file
July 30, 2020: AnnotSV version 2.4 is posted.
- Update of the annotations sources (see the corresponding README section)
- Add of the COSMIC SV dataset (Cancer)
- AnnotSV now reports either RefSeq or Ensembl gene transcripts. Use the new "-tx" option to report either NM or ENST transcripts
- The "NM" column has been renamed "tx"
- The "RefGene" directory has been renamed "Genes"
- Can be disabled in the AnnotSV configfile
- Integration of 4 Tcl packages (http/tar/csv/json) in the AnnotSV distribution
- Use of the “bcftools” toolset (Li, 2011) to fix a bug with multiallelic sites from VCF input file(s)
- bcftools is now required if using VCF input file(s)
- "1000g_AF" and "1000g_max_AF" features are not reported anymore
- Add bugfix concerning the CDS length and tx length calculation
- Add bugfix concerning annotation of 2 SV with the same coordinates but from different types (DEL, DUP...)
- Add bugfix with gzipped VCF files as input
- Add bugfix concerning the running of bash scripts (illegal use of | or |& in command)
- Add bugfix concerning the use of the "-snvIndelFiles" and "-candidateSnvIndelSamples" options
- Add bugfix to the Exomiser module
- Add bugfix concerning the AnnotSV installation when PREFIX is not the current directory
- Add bugfix concerning the use of a big "candidateGenesFile"
Dec 20, 2019: AnnotSV version 2.3 is posted.
- Include phenotype-driven annotations (HPO), based on Exomiser (Smedley et al., 2015)
- Include the lift-over GRCh38 gnomAD SV frequency annotation
- Include the "-annotationsDir" option to pass the annotations directory to AnnotSV at run time
- New "AnnotSV ID" settings (to ensure unique SV identifiers)
- Deletion filtering improvement
- Integration of the gnomAD frequency data in the ranking
- AnnotSV can now create two other output files:
- A report of unannotated variants (e.g. badly formatted SV, variant length < SVminSize...)
- A report of the decisions that explain the ranking of each SV
- vcfFiles >> snvIndelFiles
- vcfPASS >> snvIndelPASS
- vcfSamples >> snvIndelSamples)
- filteredVCFfiles >> candidateSnvIndelFiles
- filteredVCFsamples >> candidateSnvIndelSamples
- AnnotSV executable is now directly located in $ANNOTSV/bin to respect the FHS
- Add bugfix concerning the management of BED files
- Add bugfix for the report of the compound heterozygosity (1 SV + 1 SNV/indel)
- Add bugfix concerning the -candidateGenesFiltering option
- Add bugfix concerning the DGV metrics
- Add bugfix concerning the use of the "-sort" Linux command (whose behavior is OS dependant)
- Add bugfix concerning the use of "external gene annotation files"
- Add bugfix concerning the -txFile option
July 23, 2019: AnnotSV now has a dedicated profile on Twitter.
Follow AnnotSV and stay tuned with the latest news on developments (@AnnotSv)
July 9, 2019: AnnotSV code is hosted on GitHub.
July 09, 2019: AnnotSV version 2.2 is posted.
- AnnotSV follows now the Filesystem Hierarchy Standard (FHS). Installation can be easily done using a Makefile
- Include 2 new options:
- "-candidateGenesFiltering" to select the SV overlapping a gene from the "candidateGenesFile" (default = no)
- "-rankFiltering" to select the SV of a user-defined specific class (from 1 to 5), default = "1-5"
- AnnotSV is now available for the Mouse genome SV annotations
- Add the UTR/CDS's information from overlapping genes (location2 column)
- Add bugfix concerning the use of the "-candidateGenesFile" and "-reciprocal" options
- Add bugfix concerning the report of the SV length
- Add bugfix concerning the report of gene-based annotation on the full lines
Apr 18, 2019: AnnotSV version 2.1 is posted.
- Include the gnomAD SV frequency annotation
- Include the Ira M. Hall’s lab SV frequency annotations
- Include GeneHancer annotation (an integrated compendium of human promoters, enhancers and their inferred target genes)
WARNING: not supplied as part of the AnnotSV sources. Users need to request the up-to-date GeneHancer data dedicated to AnnotSV
- Include 2 new options:
- "-overwrite" to overwrite existing output results (default = yes)
- "-txFile" to specify a list of preferred genes transcripts to be used during the annotation
- Large bed annotation files are presorted, in order to be compatible for server with low specifications
- Improve error messages and exit management (return a non-zero exit code in case of error or zero if all went fine)
- AnnotSV minimum requirement is now starting with Tcl 8.5
- Add bugfix concerning the homozygous and heterozygous SNV/indel counts within the SV to annotate
- Add bugfix for the SV ranking (when the -metrics option was set to "fr")
- Add bugfix concerning the "-reciprocal" option
Dec 21, 2018: AnnotSV version 2.0 is posted.
- Add ranking/classification for SV in 5 classes (from benign to pathogenic)
- Include 12 additional annotations including:
- the creation of a unique identifier for each SV
- the SV length
- the SV type (DEL, DUP, ...)
- the SV ranking/classification
- the OMIM morbid genes
- the ClinGen Haploinsufficiency Score
- the ClinGen Triplosensitivity Score
- the ACMG genes
- the CNV intolerance from ExAC
- Add bugfix concerning empty SV input file: return a non-zero exit status (1) to continue processing in a pipeline
- Modification of the directories structure for the annotation. Please look at the README file.
- Options: "SVfromDBoverlap", "FeaturesOverlap" and "SVtoAnnOverlap" have been replaced by "reciprocal" and "overlap"
- By default, AnnotSV now reports the additional fields from the SV BED input file
- Report of the input BED file header in the output
- Update of all annotation sources provided with AnnotSV
Oct 09, 2018: AnnotSV version 1.2 is posted.
- Support the integration of user defined annotated regions imported from BED and/or TSV file(s) into the output file
- Include 3 additional output annotations columns based on the dbVar pathogenic NR SV dataset:
- The dbVar NR SV event types (e.g. deletion, duplication…)
- The dbVar NR SV accession (e.g. nssv1415016)
- The dbVar NR SV clinical assertion (e.g. pathogenic, likely pathogenic)
- OutputFile extension will always be a “.tsv” (tab separated values) extension
- Add bugfix concerning large SV and TAD boundaries annotation
May 16, 2018: AnnotSV version 1.1.1 is posted.
- Add bugfix concerning 1000g annotation (in some cases, an insertion could be not reported and AnnotSV would stop functioning properly)
Apr 11, 2018: Manuscript accepted for publication at Bioinformatics
Geoffroy V., Herenger Y., Kress A., Stoetzel C., Piton A., Dollfus H. and Muller J., AnnotSV: An integrated tool for Structural Variations annotation. Bioinformatics, 2018
Mar 20, 2018: AnnotSV version 1.1 is posted.
- Add bugfix concerning counts of the homozygous and heterozygous variants in VCF files
- Support for new SV input file format: VCF file (4.3) can now be used to describe the SV to annotate (in addition to the BED format)
The "-bedFile" option has now been renamed "-SVinputFile"
The "-bedInfo" option has now been renamed "-SVinputInfo". Default is now set to 0 (the additional fields from the SV input fi le are not reported in the outputfile)
- Report additional information while counting variants in the SNV/indel input file(s):
- The number of SNV/indel loaded
- The number of SNV/indel not considered because of the “FILTER” column value
- The number of SNV/indel not considered because of the absence of genotype information (“GT” value can be absent in bad VCF formatted files)
- The number of SV present but not considered for that purpose (only SNV/indel are taken into account)
- Include 2 new options (-outputDir and -outputFile) to specify the output directory and file name
- Include 3 additional output annotations columns based on the 1000 genomes phase 3 dataset:
- The type of event (i.e. DEL, ALU, DUP,
- The global allele frequency
- The maximum observed allele frequency across populations
Dec 21, 2017: AnnotSV version 1.0 is posted.
Copyright © 2017-present GEOFFROY Véronique
Last modified: May 25, 2023