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Question: annotation of SV (Structural Variants)
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gravatar for Bogdan
14 months ago by
Bogdan490
Palo Alto, CA, USA
Bogdan490 wrote:

Dear all,

for a list of Structural Variants (including deletions, duplications, inversions, translocations), either in VCF or BEDPE format, we would like to have the gene annotations, and the lists of the following sets of genes :

-- fusions (if both breakpoints are in exons, introns, utrs)
-- truncations (if only one breakpoint is in exon, intron, utr; and the other breakpoint is in intergenic area)
-- the genes in the areas that are deleted, duplicated, inverted

could we get all these annotations with a package in R/BioC (possibly with VariantAnnotation) ?

I wrote some scripts in perl based on Annovar, although it would be helpful to implement this in R as well.

thanks a lot,

-- bogdan

 

ADD COMMENTlink written 14 months ago by Bogdan490
1

VariantAnnotation will give you the calls but I don't think we're annotating stuff at this level. locateVariants() would be a good place to start.

ADD REPLYlink written 14 months ago by Michael Lawrence10.0k

Thanks, Mike, yes, I am looking into locateVariants(). I have the scripts in perl, although the other parts of the pipelines (especially for SNV/INDELs) is in R, and it would run smoother, shall I have the SV annotation part in R as well.

 

ADD REPLYlink modified 14 months ago • written 14 months ago by Bogdan490

Hi Mike,

talking about the annotation of the SV, Daniel Cameron mentioned that he started developing an R/BioC package :

https://github.com/PapenfussLab/StructuralVariantAnnotation

ADD REPLYlink modified 14 months ago • written 14 months ago by Bogdan490
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