SV vcf outputs to bedpe

[2nelly]

Hi all,

Does anybody have scripts to convert:

breakdancer output ----> bedpe

delly vcf ---> bedpe

Thank you all in advance!!! cheers

[dcameron]

It's not the cleanest approach for your purposes but you can do:

breakdancer->VCF using https://github.com/PapenfussLab/sv_b...kdancer2vcf.py

Then convert the VCFs (DELLY & BreakDancer) into R break-end GRanges object using https://github.com/PapenfussLab/Stru...iantAnnotation

Then convert the break-end GRanges to bedpe similar to how it is done in:

https://github.com/PapenfussLab/gridss/blob/master/example/somatic.R

That said, I've found this approach quite powerful for SV analysis as you can perform annotation and filtering on the GRanges objects in R in just a few couple of code.

[2nelly]

Thnx!

Actually, I tried a week ago the python script for breakdancer, but this is not what I was looking for.

By the way GRanges is a good approach

[dcameron]

By the way GRanges is a good approach

It's been by far the easiest approach I've found to SV annotation. My package isn't part of bioconductor yet as my linking between the two break-end for each breakpoint is just a $partner column and I suspect the BioConductor powers that be would want more S4 classes.

The real value in the package is in the GRanges conversion that works for most popular callers^, and findBreakpointOverlaps() for SV call matching.

^ I've tested breakdancer, cortex, crest, delly, gasv, gridss, hydra, lumpy, manta, pindel, socrates, tigra. It would be really nice if more callers adhered to the VCF specifications when they output VCF.