MalformedReadFilter

Filter out malformed reads.

Category Read Filters

Overview

Command-line Arguments

MalformedReadFilter specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

Name	Type	Default value	Summary
Optional
--filter_bases_not_stored	boolean	false	if a read has no stored bases (i.e. a '*'), filter out the read instead of blowing up.
-filterMBQ	boolean	false	if a read has mismatching number of bases and base qualities, filter out the read instead of blowing up.

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.

--filter_bases_not_stored / -filterNoBases ( boolean with default value false )

if a read has no stored bases (i.e. a '*'), filter out the read instead of blowing up..

-filterMBQ / --filter_mismatching_base_and_quals ( boolean with default value false )

if a read has mismatching number of bases and base qualities, filter out the read instead of blowing up..

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.