Annotation for SV and CNV
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5.0 years ago
always_learning ★ 1.1k

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

Annotation CNV SV • 6.6k views
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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).

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

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

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

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

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how annovar use?annotation sv ?

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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:

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5.0 years ago
Denise CS ★ 5.1k

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.

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

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5.0 years ago

ANNOVAR

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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?

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2.7 years ago

I use vcfanno for annotating SVs

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