Question: Annotation for SV and CNV
gravatar for always_learning
2.4 years ago by
Doha, Qatar
always_learning930 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 • 2.3k views
ADD COMMENTlink modified 7 weeks ago by WouterDeCoster34k • written 2.4 years ago by always_learning930


I'm annotating my CNV / SV human events with the AnnotSV tool:

PMID: 29669011 DOI: 10.1093/bioinformatics/bty304

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

  • ...

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

Moreover, interesting information, this tool constructs an annotation based on the full-length SV but also an annotation for each gene within the SV.

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 that share a 70% reciprocal overlap measured by length and position (> 70% shared length) (as done in DGV).

ADD REPLYlink modified 4 months ago • written 4 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 4 months ago by Bogdan680

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

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by LGMgeo90
gravatar for Denise - Open Targets
2.4 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets4.7k 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 2.4 years ago by Denise - Open Targets4.7k

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

ADD REPLYlink written 4 months ago by SmallChess460
2.4 years ago by


ADD COMMENTlink written 2.4 years ago by QVINTVS_FABIVS_MAXIMVS2.1k

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 16 months ago by fjpt.com0
gravatar for
16 months ago by
fjpt.com0 wrote:

how annovar use?annotation sv ?

ADD COMMENTlink written 16 months 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 16 months ago by WouterDeCoster34k
gravatar for WouterDeCoster
7 weeks ago by
WouterDeCoster34k wrote:

I use vcfanno for annotating SVs

ADD COMMENTlink written 7 weeks ago by WouterDeCoster34k
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