MappingQualityUnavailableFilter

Filter out reads with no mapping quality information

Category Read Filters


Overview

This filter 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 MappingQualityUnavailable
 

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GATK version 3.7-0-gcfedb67 built at 2017/02/09 12:35:06.