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 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 Flags
--filter_bases_not_stored
 -filterNoBases
false if a read has no stored bases (i.e. a '*'), filter out the read instead of blowing up.
--filter_mismatching_base_and_quals
 -filterMBQ
false if a read has mismatching number of bases and base qualities, filter out the read instead of blowing up.
--filter_reads_with_N_cigar
 -filterRNC
false filter out reads with CIGAR containing the N operator, instead of stop processing and report an error.

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

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

boolean  false


--filter_mismatching_base_and_quals / -filterMBQ

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

boolean  false


--filter_reads_with_N_cigar / -filterRNC

filter out reads with CIGAR containing the N operator, instead of stop processing and report an error.

boolean  false


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.1-1-g07a4bf8 built at 2014/03/18 07:00:36. GTD: NA