December 19, 2020: AnnotSV 3.0 is alive!

- Major code rewrite and annotations sources reorganization

- New SV ranking based on the ACMG guidelines (Riggs et al 2020) as a replacement of the previous ranking (v2.5) - Merge pathogenic SV annotation (from multiple sources) - Merge benign SV annotation (from multiple sources)
- Add pathogenic SNV/indel annotation (from ClinVar)
- 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:

- Add bugfix for exomiser use (don't use some badly formatted NCBI gene ID)
- 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

- Add of the "Samples_ID" feature (report of the sample names for which the SV was called)
- Include the new "-externalGeneFiles" option to pass external gene file(s) path in the command line
- 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)
- Fix the output columns order not being the same depending on the system environment
- "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:

- Change the names of the misleading following options:
- Annotations are not distributed anymore with the sources but downloaded during the installation with the Makefile
- 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:

- Users can now disable default annotation (through a configfile) provided by AnnotSV and only have user defined annotations
- 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:

- Default of the -SVinputInfo option is now set to 1 (the additional fields from the SV input file are reported in the outputfile)
- 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:

- Add of the "metrics" option to change numerical values to us or fr metrics (e.g. 0.2 or 0,2)
- 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:

- Include 1 new option (-typeOfAnnotation) to configure the types of lines produced by AnnotSV (both, full or split)
- 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):

- Set the default setting of the -vcfPASS option to 0 (to be non-restrictive and consider all variants in the VCF by default)
- 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: - Include a new option (-SVminSize) to set the SV minimum size (in bp). Default is 50 (bp)

Dec 21, 2017: AnnotSV version 1.0 is posted.