search

PapenfussLab / StructuralVariantAnnotation

R package designed to simplify structural variant analysis
GNU General Public License v3.0
68 stars 15 forks source link

Error loading vcf with some SV types #26

Open cboursnell opened 4 years ago

cboursnell commented 4 years ago

I have a GRIDSS vcf that I have updated the svtype field (which was all BND to start with) to be taken from the output of Clove. So these are BND, DEL, INV, TAN, TRA. When I try to load this vcf into R and get the breakpointRanges I get an error. My R is:

vcf <- readVcf(input, "hg38")
gr <- breakpointRanges(vcf)

and the error is 

Error in names(cgr)[is.na(end), ] : incorrect number of dimensions

Update: I have tried just changing the deletion events from BND to DEL and this gives the same error. I can provide a minimal reproducible example if needed.

d-cameron commented 4 years ago

Yes, please provide a minimal reproduction VCF with just one or two of the offending records.