Keep records that don't match the specified filter string(s).

Category Read Filters

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Overview

Keep records that don't match the specified filter string(s). Filter strings consist of a two character read group tag name such as "RG", "PU", etc., as defined by SAMReadGroupRecord, followed by a ":", and then the specific value to use for filtering.

For example, this filter value uses the platform unit (PU) tag: PU:1000G-mpimg-080821-1_1 to filter out reads with the read group platform unit value 1000G-mpimg-080821-1_1

ReadGroupBlackListReadFilter 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
Required Arguments
--read-group-black-list	[]	A read group filter expression in the form "attribute:value", where "attribute" is a two character read group attribute such as "RG" or "PU".

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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--read-group-black-list / NA

A read group filter expression in the form "attribute:value", where "attribute" is a two character read group attribute such as "RG" or "PU".

R List[String]  []

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GATK version 4.1.6.0-SNAPSHOT built at Thu, 2 Apr 2020 14:54:17 -0400.