Filters out reads that have greater than the threshold number of N bases
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 | |||
| --ambig-filter-bases |
Threshold number of ambiguous bases. If null, uses threshold fraction; otherwise, overrides threshold fraction. | ||
| --ambig-filter-frac |
0.05 | Threshold fraction of ambiguous bases | |
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.
Threshold number of ambiguous bases. If null, uses threshold fraction; otherwise, overrides threshold fraction.
Exclusion: This argument cannot be used at the same time as ambig-filter-frac.
Integer null
Threshold fraction of ambiguous bases
Exclusion: This argument cannot be used at the same time as ambig-filter-bases.
double 0.05 [ [ -∞ ∞ ] ]
See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum
GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.