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

Summary for GATK

args <- systemArgs(sysma="param/annotate_vars.param", mytargets="targets_gatk_filtered.txt")
varSummary(args)
write.table(varSummary(args), "./results/variantStats_gatk.xls", quote=FALSE, col.names = NA, sep="\t")

Summary for BCFtools

args <- systemArgs(sysma="param/annotate_vars.param", mytargets="targets_sambcf_filtered.txt")
varSummary(args)
write.table(varSummary(args), "./results/variantStats_sambcf.xls", quote=FALSE, col.names = NA, sep="\t")

Summary for VariantTools

args <- systemArgs(sysma="param/annotate_vars.param", mytargets="targets_vartools_filtered.txt")
varSummary(args)
write.table(varSummary(args), "./results/variantStats_vartools.xls", quote=FALSE, col.names = NA, sep="\t")



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