Annotation for SV and CNV

Question

[always_learning]

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

[LGMgeo]

Hi,

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

https://www.lbgi.fr/AnnotSV/

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).

[Bogdan]

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

[LGMgeo]

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

[jan]

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

[LGMgeo]

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

[fjpt.com]

how annovar use？annotation sv ？

[WouterDeCoster]

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.

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Answer 1

[Denise CS]

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.

[scchess]

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

Answer 2

[QVINTVS_FABIVS_MAXIMVS]

ANNOVAR

[fjpt.com]

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?

Answer 3

[WouterDeCoster]

I use vcfanno for annotating SVs