To simplify comparisons among samples, the combineVarReports function combines all variant annotation reports referenced in a SYSargs2 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 GATK

dir_path <- system.file("extdata/cwl/varseq", package = "systemPipeR")
args <- loadWorkflow(targets = "results/targets_report_gatk.txt", 
    wf_file = "combine.cwl", input_file = "varseq.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FILE1_", SampleName = "_SampleName_"))
combineDF <- combineVarReports(args, filtercol = c(Consequence = "nonsynonymous"))
write.table(combineDF, "./results/combineDF_nonsyn_gatk.xls", 
    quote = FALSE, row.names = FALSE, sep = "\t")

Combine results bcftools

args <- loadWorkflow(targets = "results/targets_report_bcf.txt", 
    wf_file = "combine.cwl", input_file = "varseq.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FILE1_", SampleName = "_SampleName_"))
combineDF <- combineVarReports(args, filtercol = c(Consequence = "nonsynonymous"))
write.table(combineDF, "./results/combineDF_nonsyn_bcf.xls", 
    quote = FALSE, row.names = FALSE, sep = "\t")



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