${arg.summary}
${arg.fulltext}
This argument supports reference-ordered data (ROD) files in the following formats: ${arg.rodTypes}
#if> <#if arg.otherArgumentRequired != "NA">Dependency: This argument requires that you also specify ${arg.otherArgumentRequired}
.
Exclusion: This argument cannot be used at the same time as ${arg.exclusiveOf}
.
The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values:
<#if arg.required != "NA"> <#if arg.required == "yes"> R #if> #if> ${arg.type} <#if arg.defaultValue?has_content> ${arg.defaultValue} #if> <#if arg.minValue?is_number> [ [ ${arg.minValue} #if> <#if arg.minRecValue?is_number> [ ${arg.minRecValue} #if> <#if arg.maxRecValue?is_number> ${arg.maxRecValue} ] #if> <#if arg.maxValue?is_number> ${arg.maxValue} ] ] #if>
#macro> <#macro relatedByType name type> <#list relatedDocs as relatedDoc> <#if relatedDoc.relation == type>${summary}
<#if group?? >${line}
This Read Filter is automatically applied to the data by the Engine before processing by ${name}.
#if> <#if (readfilters?size > 1) >These Read Filters are automatically applied to the data by the Engine before processing by ${name}.
#if>This tool can be run in multi-threaded mode using this option.
#if> <#if (parallel?size > 1)>This tool can be run in multi-threaded mode using these options.
#if>This tool does not apply any downsampling by default.
#if> <#if downsampling.by != "NONE">This tool applies the following downsampling settings by default.
This tool uses a sliding window on the reference.
This tool uses ActiveRegions on the reference.
All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
Argument name(s) | Default value | Summary |
---|
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
<#list arguments.all as arg> <@argumentDetails arg=arg/> #list> #if> <@footerInfo /> <@footerClose />