Filters out reads that have greater than the threshold number of N bases
Category Read Filters
Overview
Filters out reads that have greater than the threshold number for unknown (N) bases.AmbiguousBaseReadFilter 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 | |||
--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 |
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.
--ambig-filter-bases
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
--ambig-filter-frac
Threshold fraction of ambiguous bases
Exclusion: This argument cannot be used at the same time as ambig-filter-bases
.
double 0.05 [ [ -∞ ∞ ] ]
GATK version 4.2.6.0-SNAPSHOT built at Fri, 8 Apr 2022 12:41:23 -0700.
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