MappingQualityZeroFilter

Filter out reads with mapping quality zero

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 MappingQualityZero
 

Return to top


See also GATK Documentation Index | Tool Docs Index | Support Forum

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