Showing docs for version 3.7-0

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UnmappedReadFilter

Filter out unmapped reads

Category Read Filters

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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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