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  [ [ -∞  ∞ ] ]

---

Return to top

---

GATK version 4.2.5.0-SNAPSHOT built at Mon, 7 Feb 2022 11:18:01 -0500.