Commit 58021f71 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added newQual option

parent 58a0162c
......@@ -116,6 +116,8 @@ class GenotypeGVCFs(val parent: Configurable) extends CommandLineGATK with Scatt
@Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
var useNewAFCalculator: Boolean = config("useNewAFCalculator", default = false)
@Output
@Gather(enabled = false)
private var outputIndex: File = _
......@@ -134,6 +136,7 @@ class GenotypeGVCFs(val parent: Configurable) extends CommandLineGATK with Scatt
conditional(includeNonVariantSites, "-allSites", escape = true, format = "%s") +
conditional(uniquifySamples, "-uniquifySamples", escape = true, format = "%s") +
conditional(annotateNDA, "-nda", escape = true, format = "%s") +
conditional(useNewAFCalculator, "--useNewAFCalculator") +
optional("-hets", heterozygosity, spaceSeparated = true, escape = true, format = heterozygosityFormat) +
optional("-indelHeterozygosity", indel_heterozygosity, spaceSeparated = true, escape = true, format = indel_heterozygosityFormat) +
optional("-stand_call_conf", standard_min_confidence_threshold_for_calling, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_callingFormat) +
......
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