Filter out reads with low mapping qualities.
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
|--min_mapping_quality_score||int||20||Minimum read mapping quality required to consider a read for analysis with the HaplotypeCaller|
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.
Minimum read mapping quality required to consider a read for analysis with the HaplotypeCaller.
GATK version 2.8-1-g2a26ec9 built at 2013/12/06 16:54:02.