UnmappedReadFilter

Filter out unmapped reads

Category Read Filters


Overview

This filter recognizes the SAM flag corresponding to being unmapped. It is intended to ensure that only reads that are likely to be mapped in the right place, and therefore to be informative, will be used in analysis.

Usage example

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

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