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Annotation and Ranking of Human Structural Variations

Online annotation and ranking

Annotation and ranking of your SV are freely available online. Please, fill the form below and submit.
A job ID as well as "download" buttons will be then available to retrieve your results.

Ethics: When SV submission involves human subjects, it is the submitter's responsibility to ensure that the data and files supplied to AnnotSV protect participant privacy in accordance with all applicable laws, regulations and institutional policies. Make sure to remove any direct personal identifiers from your submission.
Your data are automatically deleted from our servers after 1 month.

Online visualization

Results are powered for visualization by knotAnnotSV.
An interactive circos plot generated by vcf2circos is also available.
"visualization" buttons will be available after the submission for both output.

Running AnnotSV 3.3.3 online

Discovering AnnotSV?
- Download a SV input file example (VCF): test.vcf
- Or ask for an automatic loading of this SV input file example (VCF):
- Or enter the coordinates of your SV of interest followed by its SV type:   




A job ID will be provided at the time of data submission. It allows you to bookmark and access the results at a later time. Moreover, the status of the job (running or finished) will be reported.

SV input file options
SV Input file: VCF (.vcf/.vcf.gz) or BED (.bed) format. Please respect the extension file.
VCF file should be compliant with the VCF v4.3. BEDPE are not accepted
.

To extract the additional SV input fields and insert the data in the output file

The column number describing the SV type (DEL, DUP...) if the input SV file is a BED.
4th column = 4
Range values: 4 or more, default = -1 (value not given)


Genome build

Number of the column reporting the samples ID for which the SV was called
(if the input SV file is a BED)
Range values: [4-[, default = 5 (Samples ID should be comma or space separated)


Phenotype-driven analysis (extracted from Exomiser) options
HPO terms list describing the phenotype of the individual being investigated
Values: use comma, semicolon or space separated class values
(e.g.: "HP:0001156,HP:0001363,HP:0011304")


General options

Changing numerical values metrics: us (0.2) or fr (0,2)


Number of bases upstream from the transcription start site

SV minimum size (in bp)

Description of the types of lines produced by AnnotSV
To select the SV of a specific class : from 1 (benign) to 5 (pathogenic); or NA
Values: use comma separated class values, or use a dash to denote a range of values, default = "1-5,NA"
( e.g.: "3,4,5" or "3-5")


To expand the "start" and "end" SV positions with the VCF confidence intervals (CIPOS, CIEND) around the breakpoints

Genes options
File containing your candidate genes (gene names can be space-separated, tabulation-separated, or line-break-separated). Only used for the ranking.

To select only the SV "split" annotations overlapping a gene from the "candidateGenesFile"

Transcripts options

Origin of the transcripts (NCBI or ENSEMBL)
To specify a list of preferred genes transcripts to be used during the annotation (optional)

Benign SV setting options
Allele frequency threshold to select the benign SV in the data sources
Range values: [0.001-0.1], default = 0.01 (i.e. 1%)


Minimum number of individuals tested to consider a benign SV for the ranking
Range values: [100-1000]

Regulatory element options

To report only the morbid, HI, TS, candidate and phenotype matched genes

To report only the genes not present in "Gene_name"

False positive deletion discovery options
VCF (.vcf/.vcf.gz) input file with SNV/indel coordinates used for false positive discovery

To only use variants from snvIndelFiles that passed all filters during the calling (FILTER column value equal to PASS)
To specify the sample names from the VCF files defined from the -snvIndelFiles option
Default: use all samples from the VCF files


Compound heterozygosity analysis options
Filtered VCF (.vcf/.vcf.gz) input file with SNV/indel coordinates used for compound heterozygotes report
To specifiy the sample names from the VCF files defined from the -candidateSnvIndelFiles option
Default: use all samples from the filtered VCF files


A job ID will be provided at the time of data submission. It allows you to bookmark and access the results at a later time.
Moreover, the status of the job (running or finished) will be reported.

Browser compatibility


OS OS version Chrome version Firefox version Microsoft Edge version Safari version
Linux 18.04.3 Ubuntu 65.0 75.0 (64 bits) not available not available
MacOS/iOS Ventura 13.1 111.0 110.0 111.0 16.2
Windows 10/11 111.0 (64 bits) 110.0 (64 bits) 110.0 (64 bits) not available

If you have any problem or question, please, feel free to create a new issue on GitHub
Copyright © 2017-present GEOFFROY Véronique

Last modified: March 30, 2023