The venn diagram utilities defined by the systemPipeR package can be used to identify common and unique variants reported for different samples and/or variant callers. The below generates a 4-way venn diagram comparing four sampes for each of the two variant callers.

args <- systemArgs(sysma="param/annotate_vars.param", mytargets="targets_gatk_filtered.txt")
varlist <- sapply(names(outpaths(args))[1:4], function(x) as.character(read.delim(outpaths(args)[x])$VARID)) vennset_gatk <- overLapper(varlist, type="vennsets") args <- systemArgs(sysma="param/annotate_vars.param", mytargets="targets_sambcf_filtered.txt") varlist <- sapply(names(outpaths(args))[1:4], function(x) as.character(read.delim(outpaths(args)[x])$VARID))
vennset_bcf <- overLapper(varlist, type="vennsets")
args <- systemArgs(sysma="param/annotate_vars.param", mytargets="targets_vartools_filtered.txt")