ReadLengthFilter

Filter out reads based on length

Category Read Filters


Overview

This filter is useful for running on only reads that are longer (or shorter) than the given threshold sizes.

Usage example

     java -jar GenomeAnalysisTk.jar \
         -T ToolName \
         -R reference.fasta \
         -I input.bam \
         -o output.file \
         -rf ReadLength \
         -minRead 50 \
         -maxRead 101
 

Command-line Arguments

ReadLengthFilter 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 Parameters
--maxReadLength
 -maxRead
0 Discard reads with length greater than the specified value
--minReadLength
 -minRead
1 Discard reads with length shorter than the specified value

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.


--maxReadLength / -maxRead

Discard reads with length greater than the specified value

R int  0  [ [ -∞  ∞ ] ]


--minReadLength / -minRead

Discard reads with length shorter than the specified value

R int  1  [ [ -∞  ∞ ] ]


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GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.