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changeLog.txt
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############################################################################################################
# AnnotSV 3.1.1 #
# #
# An integrated tool for Structural Variations annotation #
# #
# Copyright (C) 2017-2021 Veronique Geoffroy ([email protected]) #
# #
############################################################################################################
For more details, please see the README file.
November 25, 2021, AnnotSV version 3.1.1
- Add bugfix when setting the ANNOTSV global environmental variable with a final "/"
- Update the documentation, add of the AnnotSV logo
November 08, 2021, AnnotSV version 3.1
- 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
- Update the benign SV annotation method:
- 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 details in the"AnnotSV_ranking_criteria" output column: (i) detailed scoring points and (ii) remove gene names redundancy
- 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)
December 18, 2020, AnnotSV version 3.0
- Major code rewrite and annotations sources reorganization
- Significant modification of the annotations column names
- New SV ranking based on the ACMG guidelines (Riggs et al 2020) as a replacement of the previous ranking (v2.5).
- Add 3 annotation columns: AnnotSV ranking score; ranking decision criteria; AnnotSV ranking class
- Merge pathogenic SV annotation (from multiple sources)
- 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
- Merge benign SV annotation (from multiple sources)
- 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 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)
November 06, 2020, AnnotSV version 2.5.2
- Add the pLI annotation from gnomAD (pLI_gnomAD), update the pLI annotation from ExAC (pLI_ExAC)
- Add the "LOEUF_bin" annotation (gnomAD)
- Add the "tx start", "tx end" and "Number of exons" annotations
The "tx length" column has been renamed "overlapped tx length"
The "CDS length" column has been renamed "overlapped CDS length"
- If not provided, the EXOMISER_GENE_PHENO_SCORE is set to "-1.0"
- Update README.md
October 13, 2020: AnnotSV version 2.5.1
- fix: Add bugfix when the "SV type" is badly formatted
October 12, 2020: AnnotSV version 2.5
- 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 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
- 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"
- Add of the "Samples_ID" feature (report of the sample names for which the SV was called)
=> Can be disabled in the AnnotSV configfile
- 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)
=> bcftools is now required if using 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
- 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
- Change the names of the misleading following options:
vcfFiles >> snvIndelFiles
vcfPASS >> snvIndelPASS
vcfSamples >> snvIndelSamples
filteredVCFfiles >> candidateSnvIndelFiles
filteredVCFsamples >> candidateSnvIndelSamples
- 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 09, 2019: AnnotSV version 2.2
- 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"
- 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
- 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 in priority during the annotation
- 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
- 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 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
Sep 28, 2018: AnnotSV version 1.2
- Support the integration of user defined annotated regions imported from BED and/or TSV file(s) into the output file
- Include 3 additional annotations 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)
- 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
- Add bugfix concerning 1000g annotation (in some cases, an insertion could be not reported and AnnotSV stopped working properly)
Mar 20, 2018: AnnotSV version 1.1
- 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 file 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)
- Set the default value 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 annotations based on the 1000 genomes phase 3 dataset:
-> The type of event (i.e. DEL, ALU, DUP, <CN3>...)
-> The global allele frequency
-> The maximum observed allele frequency across populations
- Include a new option (-SVminSize) to set the SV minimum size (in bp). Default is 50 (bp)
Dec 21, 2017: AnnotSV version 1.0