Convert SV VCF to BEDPE Format

It can sometimes be convenient to express structural variants in BEDPE format. For such applications we recommend the script vcfToBedpe available from:

https://github.com/ctsa/svtools

This repository is forked from @hall-lab with modifications to support VCF 4.1 SV format.

BEDPE format greatly reduces structural variant information compared to the SV Caller VCF output. In particular, breakend orientation, breakend homology, and insertion sequence are lost, in addition to the ability to define fields for locus and sample specific information. For this reason, Illumina only recommends BEDPE as a temporary output for applications that require it.