The varSummary function counts the number of variants for each feature type included in the anntation reports.

Summary of variants GATK

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_"))
varSummary(args)
write.table(varSummary(args), "./results/variantStats_gatk.xls", 
    quote = FALSE, col.names = NA, sep = "\t")

Summary of variants bcf

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_"))
varSummary(args)
write.table(varSummary(args), "./results/variantStats_bcf.xls", 
    quote = FALSE, col.names = NA, sep = "\t")



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