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Filters out reads that don't overlap the specified region. NOTE: This approach to extracting overlapping reads is very slow compared to using PrintReads and -L on an indexed bam file.

Category Read Filters


A simple read filter that allows for the user to specify intervals at the filtering stage. NOTE: This class is intended to be a convenience method for the very specific case where a user might want to subset a bam file by intervals but they cannot for whatever reason index/resort the file to be sorted by position. As a consequence a file subsetted using this filter will involve reading over the entire bam input and will consequently be very slow. The preferred method for subsetting a bam file in this case is to use the -L command to subset using an index to avoid reading parts of the bam outside of the specified subset.

IntervalOverlapReadFilter 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
[] One or more genomic intervals to keep

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.

--keep-intervals / NA

One or more genomic intervals to keep

R List[String]  []

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GATK version built at Wed, 9 Oct 2019 15:19:59 -0400.