@@ -82,14 +82,17 @@ class ApplyRecalibration(val root: Configurable) extends CommandLineGATK with Sc
@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="")
/** assumeSorted should be true if the input files are already sorted (based on the position of the variants) */
@Argument(fullName="assumeSorted",shortName="assumeSorted",doc="assumeSorted should be true if the input files are already sorted (based on the position of the variants)",required=false,exclusiveOf="",validation="")
varassumeSorted:Boolean=_
/** which type of IndexCreator to use for VCF/BCF indices */
@Argument(fullName="variant_index_type",shortName="",doc="which type of IndexCreator to use for VCF/BCF indices",required=false,exclusiveOf="",validation="")
varvariant_index_type:Option[String]=None
/** the parameter (bin width or features per bin) to pass to the VCF/BCF IndexCreator */
@Argument(fullName="variant_index_parameter",shortName="",doc="the parameter (bin width or features per bin) to pass to the VCF/BCF IndexCreator",required=false,exclusiveOf="",validation="")
varvariant_index_parameter:Option[Int]=None
/** Set the minimum level of logging */
@Argument(fullName="logging_level",shortName="l",doc="Set the minimum level of logging",required=false,exclusiveOf="",validation="")
varlogging_level:String=_
/** Set the logging location */
@Output(fullName="log_to_file",shortName="log",doc="Set the logging location",required=false,exclusiveOf="",validation="")
@@ -59,13 +59,16 @@ class CombineGVCFs(val root: Configurable) extends CommandLineGATK with ScatterG
@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="")
@@ -91,12 +91,15 @@ class CombineVariants(val root: 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="")
@@ -107,11 +107,15 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
@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="")
@@ -396,15 +396,23 @@ class HaplotypeCaller(val root: 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="")
@@ -131,12 +131,16 @@ class IndelRealigner(val root: Configurable) extends CommandLineGATK with Scatte
@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="")