Keep only reads with mapping qualities within a specified range
Category Read Filters
OverviewKeep only reads with mapping qualities within a specified range.
Note: this filter is not designed to handle the unavailable mapping quality (255). Use MappingQualityAvailableReadFilter to explicitly filter out reads with unavailable quality.
See these additional references.
MappingQualityReadFilter 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 Tool Arguments|
||Maximum mapping quality to keep (inclusive)|
||10||Minimum mapping quality to keep (inclusive)|
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.
Maximum mapping quality to keep (inclusive)
Minimum mapping quality to keep (inclusive)
int 10 [ [ -∞ ∞ ] ]
GATK version 126.96.36.199-SNAPSHOT built at Fri, 24 Apr 2020 12:01:12 -0400.