Keep only reads with mapping qualities within a specified range

Category Read Filters

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Overview

Keep only reads with mapping qualities within a specified range.

Note: this filter is not designed to handle the unavailable mapping quality (255). Use MappingQualityAvailableReadFilter to explicitly filter out reads with unavailable quality.

Additional references

See these additional references.

• MappingQualityAvailableReadFilter

MappingQualityReadFilter 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
--maximum-mapping-quality	null	Maximum mapping quality to keep (inclusive)
--minimum-mapping-quality	10	Minimum mapping quality to keep (inclusive)

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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--maximum-mapping-quality / NA

Maximum mapping quality to keep (inclusive)

Integer  null

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--minimum-mapping-quality / NA

Minimum mapping quality to keep (inclusive)

int  10  [ [ -∞  ∞ ] ]

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GATK version 4.0.2.0 built at 02-13-2019 02:13:49.