<#include "common.html"/> <#macro argumentlist name myargs> <#if myargs?size != 0> ${name} <#list myargs as arg> ${arg.name} ${arg.type} ${arg.defaultValue!"NA"} ${arg.summary} <#-- < td>${arg.required} --> <#macro argumentDetails arg>

${arg.name} <#if arg.synonyms??> / ${arg.synonyms} ( <#if arg.attributes??>${arg.attributes} ${arg.type} <#if arg.defaultValue??> with default value ${arg.defaultValue} )

${arg.summary}. ${arg.fulltext} <#if arg.rodTypes??>${arg.name} binds reference ordered data. This argument supports ROD files of the following types: ${arg.rodTypes} <#if arg.options??>
The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values:

<#list arg.options as option>
${option.name}
${option.summary}

<#macro relatedByType name type> <#list relatedDocs as relatedDoc> <#if relatedDoc.relation == type>

${name}

<#break> <@makeHeader title="${name} documentation" isIndex=false />

${name}

${summary}

<#if author??>

Author ${author}

<#if group?? >

Category ${group}

<#if walkertype != "">

Traversal ${walkertype}

<#if walkertype != "">

PartitionBy ${partitiontype}

<#if annotinfo != "" >

Annotation type ${annotinfo}


Introduction

${description} <#-- Create references to additional capabilities if appropriate --> <#if readfilters?size != 0 || parallel?size != 0>

Additional Information

<#if readfilters?size != 0>

Read filters

<#if readfilters?size = 1>

This Read Filter is automatically applied to the data by the Engine before processing by ${name}.

<#if (readfilters?size > 1) >

These Read Filters are automatically applied to the data by the Engine before processing by ${name}.

<#if parallel?size != 0>

Parallelism options

<#if parallel?size == 1>

This tool can be run in multi-threaded mode using this option.

<#if (parallel?size > 1)>

This tool can be run in multi-threaded mode using these options.

<#if downsampling?size != 0>

Downsampling settings

This tool overrides the engine's default downsampling settings.

<#if refwindow?size != 0>

Window size

This tool uses a sliding window on the reference.

<#if activeregion?size != 0>

ActiveRegion settings

This tool uses ActiveRegions on the reference.

<#if extradocs?size != 0 || arguments.all?size != 0>

Command-line Arguments

<#if extradocs?size != 0>

Inherited arguments

The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).

<#-- This class is related to other documented classes via sub/super relationships --> <#if relatedDocs?? && relatedDocs?size != 0>

Related capabilities

<@relatedByType name="Superclasses" type="superclass"/> <@relatedByType name="Subclasses" type="subclass"/> <#-- Create the argument summary --> <#if arguments.all?size != 0>

${name} specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

<@argumentlist name="Required" myargs=arguments.required/> <@argumentlist name="Optional" myargs=arguments.optional/> <@argumentlist name="Advanced" myargs=arguments.advanced/> <@argumentlist name="Hidden" myargs=arguments.hidden/> <@argumentlist name="Depreciated" myargs=arguments.depreciated/>
Name Type Default value Summary
<#-- List all of the --> <#if arguments.all?size != 0> <#-- Create the argument details -->

Argument details

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/> <@footerInfo /> <@pageFooter />