To simplify comparisons among samples, the \Rfunction{combineVarReports}
function combines all variant annotation reports referenced in a
SYSargs instance (here args). At the same time the function
allows to consider only certain feature types of interest. For instance, the
below setting filtercol=c(Consequence="nonsynonymous") will include
only nonsysynonymous variances listed in the Consequence column of
the annotation reports. To omit filtering, one can use the setting
filtercol="All".
Combine results from GATK
args <- systemArgs(sysma="param/annotate_vars.param", mytargets="targets_gatk_filtered.txt")
combineDF <- combineVarReports(args, filtercol=c(Consequence="nonsynonymous"))
write.table(combineDF, "./results/combineDF_nonsyn_gatk.xls", quote=FALSE, row.names=FALSE, sep="\t")
Combine results from BCFtools
args <- systemArgs(sysma="param/annotate_vars.param", mytargets="targets_sambcf_filtered.txt")
combineDF <- combineVarReports(args, filtercol=c(Consequence="nonsynonymous"))
write.table(combineDF, "./results/combineDF_nonsyn_sambcf.xls", quote=FALSE, row.names=FALSE, sep="\t")
Combine results from VariantTools
args <- systemArgs(sysma="param/annotate_vars.param", mytargets="targets_vartools_filtered.txt")
combineDF <- combineVarReports(args, filtercol=c(Consequence="nonsynonymous"))
write.table(combineDF, "./results/combineDF_nonsyn_vartools.xls", quote=FALSE, row.names=FALSE, sep="\t")
combineDF[2:4,]