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Old 07-09-2018, 08:36 AM   #4
lgmSeq
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Location: France

Join Date: Jun 2014
Posts: 5
Default AnnotSV: An integrated tool for Structural Variations annotation

Hi,

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 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).

Last edited by lgmSeq; 07-09-2018 at 10:21 PM.
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