Describe the complexity of an assembly region

Category Variant Annotations

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Overview

AssemblyComplexity specific arguments

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
Optional Tool Arguments
--assembly-complexity-reference-mode	false	If enabled will treat the reference as the basis for assembly complexity as opposed to estimated germline haplotypes

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.

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--assembly-complexity-reference-mode

If enabled will treat the reference as the basis for assembly complexity as opposed to estimated germline haplotypes

boolean  false

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GATK version 4.4.0.0 built at Thu, 16 Mar 2023 15:00:37 -0400.