Keep only paired reads with mates mapped >= mate-too-distant-length (default 1KB) apart or on different contigs

Category Read Filters

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Overview

Keep only paired reads that are not near each other in a coordinate-sorted source of reads. (I.e., they're both mapped, but mapped to different contigs, or are mapped too far apart on the same contig.)

See MappedReadFilter for criteria defining an mapped read.

Additional references

See these additional references.

• MappedReadFilter

MateDistantReadFilter 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
--mate-too-distant-length	1000	Minimum start location difference at which mapped mates are considered distant

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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--mate-too-distant-length

Minimum start location difference at which mapped mates are considered distant

int  1000  [ [ -∞  ∞ ] ]

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GATK version 4.2.0.0-SNAPSHOT built at Mon, 22 Feb 2021 13:44:49 -0800.