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HCMappingQualityFilter

Filter out reads with low mapping qualities.

Category Read Filters


Overview


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.


--min_mapping_quality_score / -mmq

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

int  20  [ [ -?  ? ] ]


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA