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Filter out reads based on strand orientation

Category Read Filters


This filter is useful for isolating reads from only forward or reverse strands. By default, it filters out reads from the negative (reverse) strand. This logic can be reversed by using the -filterPositive flag.

Usage example

Set the read strand filter to filter out positive (forward) strand reads

     java -jar GenomeAnalysisTk.jar \
         -T ToolName \
         -R reference.fasta \
         -I input.bam \
         -o output.file \
         -rf ReadStrand \

Command-line Arguments

ReadStrandFilter 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 Flags
false Discard reads on the forward strand

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.

--filterPositive / -fp

Discard reads on the forward strand

boolean  false

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GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.