Keep only read pairs with insert length less than or equal to the given value

Category Read Filters

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Overview

Keep only read pairs (0x1) with absolute insert length less than or equal to the specified maximum, and/or greater than or equal to the specified minimum.

Taking absolute values allows inclusion of pairs where the mate of the read being considered is at a smaller genomic coordinate. Insert length is the difference between the 5' outer ends of mates, akin to a SAM record's TLEN (column 9). Length is zero for single-end reads or when the information is unavailable.

FragmentLengthReadFilter 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
--max-fragment-length	1000000	Maximum length of fragment (insert size)
--min-fragment-length	0	Minimum length of fragment (insert size)

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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--max-fragment-length

Maximum length of fragment (insert size)

int  1000000  [ [ -∞  ∞ ] ]

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--min-fragment-length

Minimum length of fragment (insert size)

int  0  [ [ -∞  ∞ ] ]

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