Note! Please use a real tool for this such as https://github.com/mkirsche/Jasmine. If you must use something along the lines of this tool, an improved and better maintained fork of this code can be found at https://github.com/papaemmelab/mergeSVvcf.

This set of routines merges VCF files by calls, labelling calls by the callers that made them in an INFO field, Callers=. Most of the work goes into normalizing SV calls, which are treated as paired of breakpoints that are equal if they fall within a user-specified window.

Here’s a very quick example of merging three VCFs;

mergevcf -l broad,dkfz,sanger -n -m 2 svs_broad.vcf svs_dkfz.vcf svs_sanger.vcf > merged_svs.vcf

where each SV is labeled by the caller that saw it, with the labels given (-l broad,dkfz,sanger) and the number of callers that saw it (-n), at least two have to see the breakpoint for it to be PASS (-m 2), and the vcf files are given.

An overview of how it works can be found on the Simpsonlab blog.