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.
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:
and the error is
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.