Showing docs for version 3.7-0

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HCMappingQualityFilter

Filter out reads with low mapping qualities for HaplotypeCaller

Category Read Filters

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Overview

This filter is applied by default for HaplotypeCaller and is designed to ensure that only reads that are likely to be informative will be used in the reassembly process. It performs the same basic function as the regular MappingQualityFilter, but it is used at specific points in the operation of HC where it is helpful to be able to apply a different quality threshold from the general case.

Usage example

Set the HC-specific mapping quality filter to filter out reads with MAPQ < 10

     java -jar GenomeAnalysisTk.jar \
         -T HaplotypeCaller \
         -R reference.fasta \
         -I input.bam \
         -o output.vcf \
         -mmq 10
 

Note that the HCMappingQuality filter itself does not need to be specified in the command line because it is set automatically for HaplotypeCaller.

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Command-line Arguments

HCMappingQualityFilter 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	20	Minimum read mapping quality required to consider a read for analysis with the HaplotypeCaller

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 analysis with the HaplotypeCaller

int  20  [ [ -∞  ∞ ] ]

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