To simplify comparisons among samples, the 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,] 



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