Showing docs for version 3.7-0

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MappingQualityFilter

Filter out reads with low mapping qualities

Category Read Filters

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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

Set the mapping quality filter to filter out reads that have MAPQ < 15

     java -jar GenomeAnalysisTk.jar \
         -T HaplotypeCaller \
         -R reference.fasta \
         -I input.bam \
         -o output.vcf \
         -rf MappingQuality \
         -mmq 15
 

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Command-line Arguments

MappingQualityFilter 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
Optional Parameters
--min_mapping_quality_score  -mmq	10	Minimum read mapping quality required to consider a read for calling

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.

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--min_mapping_quality_score / -mmq

Minimum read mapping quality required to consider a read for calling

int  10  [ [ -∞  ∞ ] ]

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