Annotation of Structural Variants and CNVs

Question

[alons]

Hi all,

We're performing NGS on cancer DNA samples with a custom panel of target regions in different genes.

Our structural variants & CNV detection pipeline currently consists of several programs such as Lumpy, Manta, Pindel, Breakdancer, Delly and CNVkit and the variants we're interested in are insertions / deletions (of all sizes), inversions, translocations, CNVs, Internal tandem-duplications and other duplications.

From your experience & knowledge, which tools do you recommend using the purpose of annotation of all sorts of structural variants and CNVs, preferably annotation of VCFs but not necessarily.

Thank you very much in advance! Alon

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I realize this has been somewhat asked before but the posts I've found were at least 2-3 years old and didn't elaborate on cancer genomics or exome sequencing.

[Zev.Kronenberg]

I think brentp is working on adding/added SV support for VCFANNO? https://github.com/brentp/vcfanno

[Amitm]

hi, Shamelessly latching on to your question. I too am looking for reliably annotating SVs (hopefully from VCFs). I am using Lumpy and Delly. thanks!

[LGMgeo]

CNV annotation can be easily automated (with OMIM, DGV, 1000g, haploinsufficiency, TAD, ... and also with your own in-house information)!

You can look at this post describing the annotSV tool: Annotation for SV and CNV

Answer 1

[QVINTVS_FABIVS_MAXIMVS]

Annovar

http://annovar.openbioinformatics.org/en/latest/

[alons]

Thanks, it looks good. Do you know any other annotators for our purposes that are more "open source"?

[QVINTVS_FABIVS_MAXIMVS]

ANNOVAR is open source what are you talking about?

[alons]

Not for service providers or commercial users, as mentioned in their download page, in red :)

If you are a commercial user/service provider, you are required to purchase a license to ANNOVAR from BIOBASE. For more information on how to obtain a commercial license please click here.

Annovar download page

[QVINTVS_FABIVS_MAXIMVS]

Ahh sorry about that. I'm in academia so I glaze over such things. If you're still interested (and have some python chops) you can adapt my CNV annotation script. https://github.com/dantaki/gtCNV

The script you want is src/vcf.py. You can re-purpose functions like geneOverlap to fit your needs. Input is generally a list of tuples; tuples usually being (chrom,start,end,type)

If you're interested in genotyping CNVs please use my program. A paper is in the works. Don't be afraid to email me if a problem comes up.

[alons]

Thanks so much! I will definitely check it out.

[QVINTVS_FABIVS_MAXIMVS]

I just edited it and now the script is src/vcf_annotate.py to avoid confusion with pyVCF

Answer 2

[geocarvalho]

I'm searching something to annotate CNV in Genome, Exome and Target sequencing. For Genome the best promise to me was ADVISER, but it's online and didn't work to me. For exome I think that cnvScan could work well. I tried Annovar and Vep, but I need more information. What are you using today?

Answer 3

[abio]

Does VEP or snpEff not do a good job at annotating structural variants from CNVkit, Manta, Lumpy?