Filter out reads with low mapping qualities.
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|
|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
int 20 [ [ -? ? ] ]
GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA