Question: Annotation for SV and CNV
gravatar for always_learning
4.0 years ago by
Doha, Qatar
always_learning1.0k wrote:

Hello Experts and Champions,

How to annotate SV and CNV vcf files generated from tools like WHAM, Delly, LUMPY, CNVNATOR, GenomeStrip etc ? I know their are plenty of tools for SNV but I am just wondering what are ways to annotate SV's ?

Thanks in advance

cnv annotation sv • 5.1k views
ADD COMMENTlink modified 21 months ago by WouterDeCoster44k • written 4.0 years ago by always_learning1.0k


CNV / SV human events can be annotated with the AnnotSV tool:

PMID: 29669011 DOI: 10.1093/bioinformatics/bty304

AnnotSV starts by detecting the genomic overlaps between the input and the annotation features.

It associates a complete panel of different datasets to provide high quality structural variations (SV) / CNV annotation :

  • Gene annotations

  • Promoters annotations

  • DGV Gold Standard annotations

  • DECIPHER gene annotations

  • 1000 genomes annotations

  • GC content annotations

  • Repeated sequences annotations

  • TAD annotations

  • OMIM annotations

  • Gene intolerance annotations

  • Haploinsufficiency annotations

  • Homozygous and heterozygous SNV/indel annotations

  • ...

Moreover, in order to help the clinical interpretation of the SV, AnnotSV provides a systematic classification of each SV into one of the following classes: class 1 (benign), class 2 (likely benign), class 3 (variant of unknown significance), class 4 (likely pathogenic) and class 5 (pathogenic).

It is also to notice that AnnotSV builds 2 types of annotations, one based on the full-length SV and one based on each gene within the SV. Thus you will have access to:

  • all the overlapped genes information (ID, OMIM...)
  • the SV location within each overlapped gene (e.g. "exon3-intron11", "txStart-intron19", ...)

Really easy to install and to use!

Input format: VCF or BED

Else, if you have CNV calls from four different CNV callers, I advise you (before to annotate) to identify/merge the common CNV detected by your different callers. For that, I would consider CNV of the same type (deletion, insertion, inversion...) that share a 70% reciprocal overlap measured by length and position (> 70% shared length) (as done in DGV).

ADD REPLYlink modified 7 months ago • written 24 months ago by LGMgeo90

Please, would you let us know, does AnnotSV also infer fusions and truncations depending on gene orientation and SV orientation ? Thank you !

ADD REPLYlink written 23 months ago by Bogdan1000

Could you please explain more? Can you give an input/output example of what you wish?

ADD REPLYlink modified 21 months ago • written 21 months ago by LGMgeo90

Is this tool suitable for SVs sequenced from PacBio long reads and called using Sniffle?

ADD REPLYlink written 8 months ago by jan130

Yes, you just need an SV input file in a VCF or BED format.

ADD REPLYlink written 7 months ago by LGMgeo90

how annovar use?annotation sv ?

ADD REPLYlink written 3.0 years ago by fjpt.com0

You'll need to put more effort in your question and elaborate on the data you have, what you tried and what didn't work, with commands and error messages.

Welcome to biostars. Interesting guidelines for posting can be found in the following posts:

ADD REPLYlink written 3.0 years ago by WouterDeCoster44k
gravatar for Denise - Open Targets
4.0 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.1k wrote:

Try the Variant Effect Predictor, or VEP. It does annotate both Structural variants and SNVs. It's available as an online tool, Perl script or through the Ensembl Rest API.

ADD COMMENTlink written 4.0 years ago by Denise - Open Targets5.1k

Not really. VEP doesn't support the very common BND SVType.

ADD REPLYlink written 24 months ago by SmallChess510
4.0 years ago by


ADD COMMENTlink written 4.0 years ago by QVINTVS_FABIVS_MAXIMVS2.4k

Data generated from CREST,and i want to annotation it like snp ,because I saw someone else do that,Can you give me an example?

ADD REPLYlink written 3.0 years ago by fjpt.com0
gravatar for WouterDeCoster
21 months ago by
WouterDeCoster44k wrote:

I use vcfanno for annotating SVs

ADD COMMENTlink written 21 months ago by WouterDeCoster44k
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