Keep only paired reads with mates mapped >= mate-too-distant-length (default 1KB) apart or on different contigs
Category Read Filters
OverviewKeep 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.
See these additional references.
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|
||1000||Minimum start location difference at which mapped mates are considered distant|
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.
Minimum start location difference at which mapped mates are considered distant
int 1000 [ [ -∞ ∞ ] ]
GATK version 22.214.171.124-SNAPSHOT built at Wed, 13 Apr 2022 13:12:10 -0700.